Merge branch 'cli/apply-text-edit' into cli/lint

1.  Renamed initializeNoteGraph.ts to initialize-note-graph.ts to be consistent with naming

2.  Refactored code in janitor and migrate commands

.all-contributorsrc

@@ -241,80 +241,6 @@
         "code",
         "doc"
       ]
-    },
-    {
-      "login": "chirag-singhal",
-      "name": "CHIRAG SINGHAL",
-      "avatar_url": "https://avatars3.githubusercontent.com/u/42653703?v=4",
-      "profile": "https://github.com/chirag-singhal",
-      "contributions": [
-        "code"
-      ]
-    },
-    {
-      "login": "lostintangent",
-      "name": "Jonathan Carter",
-      "avatar_url": "https://avatars3.githubusercontent.com/u/116461?v=4",
-      "profile": "https://github.com/lostintangent",
-      "contributions": [
-        "doc"
-      ]
-    },
-    {
-      "login": "synesthesia",
-      "name": "Julian Elve",
-      "avatar_url": "https://avatars3.githubusercontent.com/u/181399?v=4",
-      "profile": "https://www.synesthesia.co.uk",
-      "contributions": [
-        "doc"
-      ]
-    },
-    {
-      "login": "thomaskoppelaar",
-      "name": "Thomas Koppelaar",
-      "avatar_url": "https://avatars3.githubusercontent.com/u/36331365?v=4",
-      "profile": "https://github.com/thomaskoppelaar",
-      "contributions": [
-        "question",
-        "code",
-        "userTesting"
-      ]
-    },
-    {
-      "login": "MehraAkshay",
-      "name": "Akshay",
-      "avatar_url": "https://avatars1.githubusercontent.com/u/8671497?v=4",
-      "profile": "http://www.akshaymehra.com",
-      "contributions": [
-        "code"
-      ]
-    },
-    {
-      "login": "johnlindquist",
-      "name": "John Lindquist",
-      "avatar_url": "https://avatars0.githubusercontent.com/u/36073?v=4",
-      "profile": "http://johnlindquist.com",
-      "contributions": [
-        "doc"
-      ]
-    },
-    {
-      "login": "epicfaace",
-      "name": "Ashwin Ramaswami",
-      "avatar_url": "https://avatars2.githubusercontent.com/u/1689183?v=4",
-      "profile": "https://ashwin.run/",
-      "contributions": [
-        "doc"
-      ]
-    },
-    {
-      "login": "Klaudioz",
-      "name": "Claudio Canales",
-      "avatar_url": "https://avatars1.githubusercontent.com/u/632625?v=4",
-      "profile": "https://github.com/Klaudioz",
-      "contributions": [
-        "doc"
-      ]
     }
   ],
   "contributorsPerLine": 7,

.github/workflows/foam-cli.yml

@@ -1,25 +0,0 @@
-name: Test foam-cli
-
-on:
-  pull_request:
-    paths:
-      - 'packages/foam-cli/**'
-  push:
-    paths:
-      - 'packages/foam-cli/**'
-
-jobs:
-  test:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v1
-      - uses: actions/setup-node@v1
-
-      - name: Install dependencies
-        run: yarn
-
-      # - name: Lint foam-lint
-      #   run: yarn workspace foam-cli lint
-
-      - name: Test foam-cli
-        run: yarn workspace foam-cli test

.github/workflows/foam-core.yml

@@ -1,25 +0,0 @@
-name: Test foam-core
-
-on:
-  pull_request:
-    paths:
-      - 'packages/foam-core/**'
-  push:
-    paths:
-      - 'packages/foam-core/**'
-
-jobs:
-  test:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v1
-      - uses: actions/setup-node@v1
-
-      - name: Install dependencies
-        run: yarn
-
-      - name: Lint foam-core
-        run: yarn workspace foam-core lint
-
-      - name: Test foam-core
-        run: yarn workspace foam-core test

.github/workflows/foam-vscode.yml

@@ -1,29 +0,0 @@
-name: Test foam-vscode
-
-on:
-  pull_request:
-    paths:
-      - 'packages/foam-vscode/**'
-  push:
-    paths:
-      - 'packages/foam-vscode/**'
-
-jobs:
-  test:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v1
-      - uses: actions/setup-node@v1
-
-      - name: Install dependencies
-        run: yarn
-
-      - name: Lint foam-vscode
-        run: yarn workspace foam-vscode lint
-      # - name: Test foam-vscode
-      #   run: yarn workspace foam-vscode test
-      # - name: Publish foam-vscode
-      #   if: github.ref == 'refs/heads/master'
-      #   run: yarn workspace foam-vscode publish-extension
-      #   with:
-      #     vsce_token: ${{ secrets.VSCE_TOKEN }}

.vscode/launch.json

@@ -6,9 +6,10 @@
 	"version": "0.2.0",
 	"configurations": [
 		{
-			// NOTE: Remember to synchronize this with the "No Build"-variant!
-			"name": "Run VSCode Extension",
-			"type": "extensionHost",
+             // This task is also defined in packages/foam-vscode/.vscode/launch.json
+             // for when running separately outside of the monorepo environment
+			"name": "Run Extension",
+            "type": "extensionHost",
 			"request": "launch",
 			"runtimeExecutable": "${execPath}",
 			"args": [
@@ -17,11 +18,12 @@
 			"outFiles": [
 				"${workspaceFolder}/packages/foam-vscode/out/**/*.js"
 			],
-			"preLaunchTask": "${defaultBuildTask}"
+			"preLaunchTask": "Build foam-vscode"
 		},
 		{
-			// NOTE: Remember to synchronize this with the "No Build"-variant!
-			"name": "Test VSCode Extension",
+            // This task is also defined in packages/foam-vscode/.vscode/launch.json
+            // for when running separately outside of the monorepo environment
+			"name": "Extension Tests",
 			"type": "extensionHost",
 			"request": "launch",
 			"runtimeExecutable": "${execPath}",
@@ -32,51 +34,12 @@
 			"outFiles": [
 				"${workspaceFolder}/packages/foam-vscode/out/test/**/*.js"
 			],
-			"preLaunchTask": "${defaultBuildTask}"
+			"preLaunchTask": "Build foam-vscode"
 		},
 		{
-			// NOTE: Remember to synchronize this with the "No Build"-variant!
-			"name": "Test Core",
-			"type": "node",
-			"request": "launch",
-			"program": "${workspaceFolder}/node_modules/tsdx/dist/index.js",
-			"args": ["test"],
-			"cwd": "${workspaceFolder}/packages/foam-core",
-			"internalConsoleOptions": "openOnSessionStart",
-			"preLaunchTask": "${defaultBuildTask}"
-		},
-		{
-			// NOTE: Remember to synchronize this with the default-variant!
-			"name": "Run VSCode Extension (No Build)",
-			"type": "extensionHost",
-			"request": "launch",
-			"runtimeExecutable": "${execPath}",
-			"args": [
-				"--extensionDevelopmentPath=${workspaceFolder}/packages/foam-vscode"
-			],
-			"outFiles": [
-				"${workspaceFolder}/packages/foam-vscode/out/**/*.js"
-			]
-		},
-		{
-			// NOTE: Remember to synchronize this with the default-variant!
-			"name": "Test VSCode Extension (No Build)",
-			"type": "extensionHost",
-			"request": "launch",
-			"runtimeExecutable": "${execPath}",
-			"args": [
-				"--extensionDevelopmentPath=${workspaceFolder}/packages/foam-vscode",
-				"--extensionTestsPath=${workspaceFolder}/packages/foam-vscode/out/test/suite/index"
-			],
-			"outFiles": [
-				"${workspaceFolder}/packages/foam-vscode/out/test/**/*.js"
-			]
-		},
-		{
-			// NOTE: Remember to synchronize this with the default-variant!
-			"name": "Test Core (No Build)",
 			"type": "node",
 			"request": "launch",
+			"name": "Workspace Manager tests",
 			"program": "${workspaceFolder}/node_modules/tsdx/dist/index.js",
 			"args": ["test"],
 			"cwd": "${workspaceFolder}/packages/foam-core",

.vscode/tasks.json

@@ -4,17 +4,18 @@
 	"version": "2.0.0",
 	"tasks": [
 		{
-			"label": "Build foam",
-			"type": "npm",
-			"script": "build",
-			"problemMatcher": "$tsc",
-			"isBackground": false,
+            // This task is also defined in packages/foam-vscode/.vscode/tasks.json
+            // for when running separately outside of the monorepo environment
+            "type": "npm",
+            "script": "watch",
+            "label": "Build foam-vscode",
+            "path": "packages/foam-vscode",
+            "problemMatcher": "$tsc-watch",
+			"isBackground": true,
 			"presentation": {
-				"reveal": "always"
-			},
-			"group": {
-				"kind": "build",
-				"isDefault": true
+				"reveal": "silent",
+				"revealProblems": "onProblem",
+				"focus": true
 			}
 		}
 	]

docs/.vscode/settings.json

@@ -5,7 +5,6 @@
   "editor.overviewRulerBorder": false,
   "editor.lineHeight": 24,
   "workbench.colorTheme": "Gray Matter Light",
-  "vscodeMarkdownNotes.noteCompletionConvention": "noExtension",
   "[markdown]": {
     "editor.quickSuggestions": {
       "other": true,

docs/_layouts/foam.html

@@ -1,35 +0,0 @@
----
-layout: default
----
-
-<script type="text/javascript">
-// NOTE: this should be in sync with the settings/usage in the vscode extension
-// atm it's just a wide superset of md extensions to cover a wide range of cases
-var MD_EXT = ['.md', '.markdown', '.mdx', '.mdown', '.mkdn', '.mkd', '.mdwn', '.mdtxt', '.mdtext', '.text', '.Rmd'];
-function normalizeMdLink(link) {
-  var url = new URL(link);
-  var mdFileExt = MD_EXT.find(ext => url.pathname.endsWith(ext));
-  if (mdFileExt) {
-    url.pathname = url.pathname.slice(0, mdFileExt.length * -1);
-  }
-  return url.toString();
-}
-
-window.addEventListener('DOMContentLoaded', (event) => {
-  document
-    .querySelectorAll(".markdown-body a[title]:not([href^=http])")
-    .forEach((a) => {
-      // Hack: Replace page-link with "Page Title"...
-      a.innerText = a.title;
-      // ...and normalize the links to allow html pages navigation
-      a.href = normalizeMdLink(a.href);
-    });
-
-  document.querySelectorAll(".github-only").forEach((el) => {
-    el.remove();
-  });
-});
-</script>
-
-
-{{ content }}

docs/_layouts/home.html

@@ -1,16 +1,25 @@
 ---
-layout: foam
+layout: default
 ---
 
 <script async defer src="https://buttons.github.io/buttons.js"></script>
 
 {{ content }}
 
-<script>
-window.addEventListener('DOMContentLoaded', (event) => {
+<script type="text/javascript">
+  // Hack: Replace page-link with "Page Title"
+  document
+    .querySelectorAll(".markdown-body a[title]:not([href^=http])")
+    .forEach((a) => {
+      a.innerText = a.title;
+    });
+
+  document.querySelectorAll(".github-only").forEach((el) => {
+    el.remove();
+  });
+
   var duplicateHeading = document.querySelector("h1:not(#foam)");
   if (duplicateHeading && duplicateHeading.remove) {
     duplicateHeading.remove();
   }
-});
 </script>

docs/_layouts/mathjax.html

@@ -1,9 +1,22 @@
 ---
-layout: foam
+layout: default
 ---
 
 {{ content }}
 
+<script type="text/javascript">
+  // Hack: Replace page-link with "Page Title"
+  document
+    .querySelectorAll(".markdown-body a[title]:not([href^=http])")
+    .forEach((a) => {
+      a.innerText = a.title;
+    });
+
+  document.querySelectorAll(".github-only").forEach((el) => {
+    el.remove();
+  });
+</script>
+
 <script src="https://cdn.jsdelivr.net/npm/mathjax@2/MathJax.js?config=TeX-AMS-MML_HTMLorMML" type="text/javascript"></script>
 <script type="text/x-mathjax-config">
     MathJax.Hub.Config({

docs/_layouts/page.html

@@ -1,5 +1,18 @@
 ---
-layout: foam
+layout: default
 ---
 
 {{ content }}
+
+<script type="text/javascript">
+  // Hack: Replace page-link with "Page Title"
+  document
+    .querySelectorAll(".markdown-body a[title]:not([href^=http])")
+    .forEach((a) => {
+      a.innerText = a.title;
+    });
+
+  document.querySelectorAll(".github-only").forEach((el) => {
+    el.remove();
+  });
+</script>

docs/azure-devops-wiki.md

@@ -1,34 +0,0 @@
-# Azure DevOps Wiki
-
-Publish your Foam workspace as an Azure DevOps wiki.
-
-[Azure DevOps](https://azure.microsoft.com/en-us/services/devops/) is Microsoft's collaboration software for software development teams, formerly known as Team Foundation Server (TFS) and Visual Studio Team Services. It is available as an on-premise or SaaS version. The following recipe was tested with the SaaS version, but should work the same way for the on-premise.
-
-The following recipe is written with the assumption that you already have an [Azure DevOps](https://azure.microsoft.com/en-us/services/devops/) project.
-
-## Setup a Foam workspace
-
-1. Generate a Foam workspace using the [foam-template project](https://github.com/foambubble/foam-template). 
-2. Change the remote to a git repository in Azure DevOps, or copy all the files into a new Azure DevOps git repository.
-3. Define which document will be the wiki home page. To do that, create a file called `.order` in the Foam workspace root folder, with first line being the document filename without `.md` extension. For a project created from the Foam template, the file would look like this:
-```
-readme
-```
-4. Push the repository to remote in Azure DevOps.
-
-## Publish repository to a wiki
-
-
-1. Navigate to your Azure DevOps project in a web browser.
-2. Choose **Overview** > **Wiki**. If you don't have wikis for your project, choose **Publish code as a wiki** on welcome page. 
-3. Choose repository with your Foam workspace, branch (usually `master` or `main`), folder (for workspace created from foam-template it is `/`), and wiki name, and press **Publish**.
-
-A published workspace looks like this:
-
-![Azure DevOps wiki](assets/images/azure-devops-wiki-demo.png)
-
-There is default table of contents pane to the left of the wiki content. Here, you'll find a list of all directories that are present in your Foam workspace, and all wiki pages. Page names are derived from files names, and they are listed in alphabetical order. You may reorder pages by adding filenames without `.md` extension to `.order` file. 
-
-_Note that first entry in `.order` file defines wiki's home page._
-
-For more information, read the [Azure DevOps documentation](https://docs.microsoft.com/en-us/azure/devops/project/wiki/publish-repo-to-wiki). 

docs/backlinking.md

@@ -9,7 +9,6 @@ When using [[wiki-links]], you can find all notes that link to a specific note i
 
 [//begin]: # "Autogenerated link references for markdown compatibility"
 [wiki-links]: wiki-links "Wiki Links"
-[make-backlinks-more-prominent]: make-backlinks-more-prominent "Make Backlinks More Prominent"
 [materialized-backlinks]: materialized-backlinks "Materialized Backlinks (stub)"
 [roadmap]: roadmap "Roadmap"
 [//end]: # "Autogenerated link references"

docs/capture-notes-with-drafts-pro.md

@@ -1,142 +0,0 @@
-# Capture Notes With Drafts Pro
-
-## Context
-
-* You use [Foam for VSCode](https://marketplace.visualstudio.com/items?itemName=foam.foam-vscode) to manage your notes
-* You wish to adopt a practice such as [A writing inbox for transient and incomplete notes](https://notes.andymatuschak.org/A%20writing%20inbox%20for%20transient%20and%20incomplete%20notes)
-* You wish to use [Drafts Pro](https://docs.getdrafts.com/) to capture quick notes into your Foam notes from your iOS device
-
-## Required Extensions
-
-* [Foam for VSCode](https://marketplace.visualstudio.com/items?itemName=foam.foam-vscode)
-
-## Other tools
-
-* We assume you are familiar with how to use GitHub (if you are using Foam this is implicit)
-* You have an iOS device with [Drafts](https://getdrafts.com/)
-* You have upgraded to [Drafts Pro](https://docs.getdrafts.com/draftspro) (needed to edit actions).
-
-## Instructions
-
-1. [Create a new action in Drafts](https://docs.getdrafts.com/docs/actions/editing-actions)
-2. Add a single [step](https://docs.getdrafts.com/actions/steps/) of type Script
-3. Edit the script adding the code from the block below
-4. Edit settings at the top of the script to suit your preferences
-5. Set other Action options in Drafts as you wish
-6. Save the Action
-7. In GitHub [create a Personal Access Token](https://github.com/settings/tokens) and give it `repo` scope - make a note of the token
-8. In Drafts create a note
-9. Select the action you created in steps 1-6
-10. On the first run you will need to add the following information:
-    1. your GitHub username
-    2. the repository name of your Foam repo
-    3. the GitHub access token from step 7
-    4. An author name
-11. Check your Github repo for a commit
-12. If you are publishing your Foam to the web you may want to edit your publishing configuration to exclude inbox files - as publishing (and method) is a user choice that is beyond the scope of this recipe
-
-## Code for Drafts Action
-
-```javascript
-// adapted from https://forums.getdrafts.com/t/script-step-post-to-github-without-working-copy/3594
-// post to writing inbox in Foam digital garden
-
-/*
- * edit these lines to suit your preferences
- */
-const inboxFolder = "inbox/";   // the folder in your Foam repo where notes are saved. MUST have trailing slash, except for root of repo use ''
-const requiredTags = ['inbox']; // all documents will have these added in addition to tags from the Drafts app
-const addLinkToInbox = true;    // true = created note will have link to [[index]], false = no link
-const addTimeStamp = true;      // true = add a note of capture date/time at foot of note
-
-/*
- * stop editing
- */
-
-const credential = Credential.create("GitHub garden repo", "The repo name, and its credentials, hosting your Foam notes");
-credential.addTextField("username", "GitHub Username");
-credential.addTextField('repo', 'Repo name');
-credential.addPasswordField("key", "GitHub personal access token");
-credential.addTextField('author', 'Author');
-credential.authorize();
-
-const githubKey = credential.getValue('key');
-const githubUser = credential.getValue('username');
-const repo = credential.getValue('repo');
-const author = credential.getValue('author');
-
-const http = HTTP.create(); // create HTTP object
-const base = 'https://api.github.com';
-
-
-const posttime = new Date();
-const title = draft.title;  
-const txt = draft.processTemplate("[[line|3..]]");
-const mergedTags = [...draft.tags, ...requiredTags];
-const slugbase = title.toLowerCase().replace(/\s/g, "-");
-
-const datestr = `${posttime.getFullYear()}-${pad(posttime.getMonth() + 1)}-${pad(posttime.getDate())}`;
-const timestr = `${pad(posttime.getHours())}:${pad(posttime.getMinutes())}:00`;
-const yr = `${posttime.getFullYear()}`;
-const pdOffset = posttime.getTimezoneOffset();
-const offsetChar = pdOffset >= 0 ? '-' : '+';
-var pdHours = Math.floor(pdOffset/60);
-console.log(pdHours);
-pdHours = pdHours >= 0 ? pdHours : pdHours * -1;
-console.log(pdHours);
-const tzString = `${offsetChar}${pad(pdHours)}:00`;
-const postdate = `${datestr}T${timestr}${tzString}`;
-
-
-const slug = `${slugbase}`
-const fn = `${slug}.md`;
-let preamble = `# ${title} \n\n`;
-
-mergedTags.forEach(function(item,index){
-   preamble += `#${item} `;
-  }
-);
-
-if (addLinkToInbox) {
-    preamble += "\n\n[[inbox]]\n";
-}
-
-preamble += "\n\n";
-
-var doc = `${preamble}${txt}`;
-
-if (addTimeStamp){
-
-    doc += `\n\nCaptured: ${postdate}\n`
-}
-
-const options = {
-    url: `https://api.github.com/repos/${githubUser}/${repo}/contents/${inboxFolder}${fn}`,
-    method: 'PUT',
-    data: {
-        message: `Inbox from Drafts ${datestr}`,
-        content: Base64.encode(doc)
-    },
-    headers: {
-        'Authorization': `token ${githubKey}`
-    }
-};
-
-var response = http.request(options);
-
-if (response.success) {
-    // yay
-} else {
-    console.log(response.statusCode);
-    console.log(response.error);
-}
-
-function pad(n) {
-    let str = String(n);
-    while (str.length < 2) {
-        str = `0${str}`;
-    }
-    return str;
-}
-
-```

docs/cli.md

@@ -9,5 +9,7 @@ Create a CLI tool to allow running common Foam commands. These may include:
 More commands to be added.
 
 [//begin]: # "Autogenerated link references for markdown compatibility"
-[workspace-janitor]: workspace-janitor "Janitor"
+[todo]: todo "Todo"
+[roadmap]: roadmap "Roadmap"
+[workspace-janitor]: workspace-janitor "Workspace Janitor (stub)"
 [//end]: # "Autogenerated link references"

docs/code-of-conduct.md

@@ -129,4 +129,6 @@ For answers to common questions about this code of conduct, see the FAQ at
 https://www.contributor-covenant.org/faq. Translations are available at
 https://www.contributor-covenant.org/translations.
 
-
+[//begin]: # "Autogenerated link references for markdown compatibility"
+[todo]: todo "Todo"
+[//end]: # "Autogenerated link references"

docs/contribution-guide.md

@@ -2,12 +2,12 @@
 
 > [[todo]] [[good-first-task]] This contribution guide itself could be improved 😅
 
-Foam is open to contributions of any kind, including but not limited to code, documentation, ideas, and feedback. Here are some general tips on how to get started on contributing to Foam:
+Foam is open to contributions of any kind, including but not limited to code, documentation, ideas and feedback. Here are some general tips on how to get started on contributing to Foam:
 
 - Use Foam for yourself, figure out what could be improved.
 - Check out [[roadmap]] to see what's already in the plans. I have thoughts about how to implement some of these, but open to ideas and code contributions!
 - Read about our [[principles]] to understand Foam's philosophy and direction
-- Read and act in accordance with our [[code-of-conduct]].
+- Read and act in accordance of our [[code-of-conduct]].
 - Feel free to open [GitHub issues](https://github.com/foambubble/foam/issues) to give me feedback and ideas for new features.
 - Foam code and documentation live in the monorepo at [foambubble/foam](https://github.com/foambubble/foam/)
   - [/docs](https://github.com/foambubble/foam/docs): documentation and [[recipes]]

docs/creating-a-new-language.md

@@ -1,5 +1,3 @@
-# Creating a New Language
-
 ## Creating a new language
 
 What if we created a new language that made it more ergonomic to use VS Code as a Foam workspace

docs/daily-notes.md

@@ -1,46 +1,36 @@
 # Daily notes
 
-Automatically create a Daily Note by executing the "Foam: Open Daily Note" command. If a Daily Note for today's date already exists, the command opens the existing note.
+The idea is to make it easier for people to be able to create Daily notes.
 
-![Daily note feature in action](assets/images/daily-note.gif)
+This feature is open for discussion at [foambubble/foam#54](https://github.com/foambubble/foam/issues/54).
 
-## Keyboard shortcut
+## Must have
 
-The default keyboard shortcut for "Open Daily Note" is `alt`+`d`. This can be overridden using the [VS Code Keybindings editor](https://code.visualstudio.com/docs/getstarted/keybindings).
+- Should exist as part of [foam-vscode](https://github.com/foambubble/foam/tree/master/packages/foam-vscode) extension 
+- A new command "Foam: Open Daily Note", which creates new file and focuses into it, or opens the existing file for today if it exists already.
+  - File should have a Level 1 `# Heading`
+- Extension should define a hotkey for it (TBD? What do other apps do?)
 
-## Configuration
+## Should have
 
-By default, Daily Notes will be created in a file called `yyyy-mm-dd.md` in the workspace root, with a heading `yyyy-mm-dd`. 
+- Settings to customise:
+  - Format of file name, default to `yyyy-mm-dd`
+  - Format of title
+    - Default to same as file name
+    - Allow override e.g. `MMMMM D, YYYY`, to July 8. 2020 (locale specific)
+  - Extension of file, default to `.md`
+  - Directory into which file should be created, default to `./` (workspace root)
+    - Should create directory if needed
 
-These settings can be overridden in your workspace or global `.vscode/settings.json` file, using the [**dateformat** date masking syntax](https://github.com/felixge/node-dateformat#mask-options):
+## Could have
+- Automatically update a "daily notes" index file, newest first. Format TBD
+  - A custom note template .md file that could be stored in `.vscode/` directory (would supercede having to format the title)
+    - This could be useful for people who e.g. want there to be a format for every day's notes with fixed questions and stuff.
+  - Maybe we could do it with just back links or tags, by putting e.g. `[[daily]]` into the note template
+  - If files were named in alphabetic sortable order, and back links would display in reverse order, newest would always come on top
 
-```json
-  "foam.openDailyNote.directory": "journal",
-  "foam.openDailyNote.filenameFormat": "'daily-note'-yyyy-mm-dd",
-  "foam.openDailyNote.fileExtension": "mdx",
-  "foam.openDailyNote.titleFormat": "'Journal Entry, ' dddd, mmmm d",
-```
+[//begin]: # "Autogenerated link references for markdown compatibility"
+[todo]: todo "Todo"
+[roadmap]: roadmap "Roadmap"
+[//end]: # "Autogenerated link references"
 
-The above configuration would create a file `journal/note-2020-07-25.mdx`, with the heading `Journal Entry, Sunday, July 25`.
-
-## Daily Note Templates
-
-In the future, Foam may provide a functionality for specifying a template for new Daily Notes and other types of documents.
-
-In the meantime, you can use [VS Code Snippets](https://code.visualstudio.com/docs/editor/userdefinedsnippets) for defining your own Daily Note template.
-
-## Roam-style Automatic Daily Notes
-
-In the future, Foam may provide an option for automatically opening your Daily Note when you open your Foam workspace.
-
-If you want this behaviour now, you can use the excellent [Auto Run Command](https://marketplace.visualstudio.com/items?itemName=gabrielgrinberg.auto-run-command#review-details) extension to run the "Open Daily Note" command upon entering a Foam workspace by specifying the following configuration in your `.vscode/settings.json`:
-
-```json
-  "auto-run-command.rules": [
-    {
-      "condition": "hasFile: .vscode/foam.json",
-      "command": "foam-vscode.open-daily-note",
-      "message": "Have a nice day!"
-    }
-  ],
-```

docs/diagrams-in-markdown.md

@@ -12,6 +12,7 @@ You can use VS Code plugins such as [Mermaid](https://marketplace.visualstudio.c
 
 [//begin]: # "Autogenerated link references for markdown compatibility"
 [github-pages]: github-pages "Github Pages"
-[todo]: todo "Todo"
 [good-first-task]: good-first-task "Good First Task"
+[todo]: todo "Todo"
+[contribution-guide]: contribution-guide "Contribution Guide"
 [//end]: # "Autogenerated link references"

docs/eleventy-and-netlify.md

@@ -10,7 +10,7 @@ With this template you can
 
 When you're ready to publish, import the GitHub repository you created with **foam-eleventy-template** into your Netlify account. (Create one if you don't have it already.)
 
-Once that's done, all you have to do is make changes to your workspace in VS Code and push them to the main branch on GitHub. Netlify will recognize the changes, deploy them automatically and give you a link where your Foam is published.
+Once that's done, all you have to do is make changes to your workspace in VS COde and push them to the main branch on GitHub. Netlify will recognize the changes, deploy them automatically and give you a link where your Foam is published.
 
 
 That's it!

docs/foam-core.md

@@ -96,11 +96,10 @@ Useful for knowing what needs to be supported. See [[feature-comparison]].
 - [[foam-core-2020-07-11]]
 
 [//begin]: # "Autogenerated link references for markdown compatibility"
-[workspace-janitor]: workspace-janitor "Janitor"
+[workspace-janitor]: workspace-janitor "Workspace Janitor"
 [cli]: cli "Command Line Interface"
 [build-vs-assemble]: build-vs-assemble "Build vs Assemble"
 [wiki-links]: wiki-links "Wiki Links"
-[link-reference-definitions]: link-reference-definitions "Link Reference Definitions"
 [materialized-backlinks]: materialized-backlinks "Materialized Backlinks (stub)"
 [todo]: todo "Todo"
 [feature-comparison]: feature-comparison "Feature comparison"

docs/foam-file-format.md

@@ -17,6 +17,8 @@ Here are a few specific constraints, mainly because our tooling is a bit fragmen
 - **In addition to normal Markdown Links syntax you can use `[[media-wiki]]` links.** See [[wiki-links]] for more details.
 
 [//begin]: # "Autogenerated link references for markdown compatibility"
-[decision-needed]: decision-needed "Decision Needed"
 [wiki-links]: wiki-links "Wiki Links"
+[github-pages]: github-pages "Github Pages"
+[decision-needed]: decision-needed "Decision Needed"
+[daily-notes]: daily-notes "Daily notes"
 [//end]: # "Autogenerated link references"

docs/gistpad.md

@@ -1,51 +0,0 @@
-# GistPad
-
-[GistPad](https://aka.ms/gistpad) is a Visual Studio Code extension that allows you to edit your GitHub gists and repos, without needing to clone anything locally. It provides support for editing Foam workspaces, complete with `[[link]]` [completion/navigation](https://github.com/vsls-contrib/gistpad#links), [daily pages](https://github.com/vsls-contrib/gistpad#daily-pages), [pasting images](https://github.com/vsls-contrib/gistpad#pasting-images-1) and [backlinks](https://github.com/vsls-contrib/gistpad#backlinks). If you'd like to persist your notes in a GitHub repository, and automatically sync changes without needing to manually commit/push/pull, then GistPad might be an option worth exploring.
-
-<img width="700px" src="https://user-images.githubusercontent.com/116461/87234714-96ba9400-c388-11ea-92c3-544d9a3bb633.png" />
-
-## Getting started
-
-To start using GistPad for your Foam-based knowledge base, simply perform the following steps:
-
-1. Download the [GistPad extension](https://aka.ms/gistpad) and then re-start Visual Studio Code
-
-1. Run the `GistPad: Sign In` command, and provide a [GitHub token](https://github.com/settings/tokens/new) that includes the `repo` scope (and optionally `gist` and `delete_repo` scope, if you'd like to use GistPad for managing your GitHub content more holistically)
-
-1. Run the `GistPad: Manage Repository` command and select the `Create repo from template...` or `Create private repo from template...` depending on your preference
-
-1. Select the `Foam-style wiki` template, and then specify a name for your Foam workspace (e.g. `my-foam-notes`, `johns-knowledge-base`)
-
-Your new repo will be created in your GitHub account, and the `Foam` welcome page will be automatically opened. If you already have an existing Foam workspace in GitHub, then when you run step #3 above, simply select or specify the name of the GitHub repository instead.
-
-> Note: If you have any and all feedback on how GistPad can be improved to support your Foam workflow, please don't hesitate to [let us know](https://github.com/vsls-contrib/gistpad)! 👍
-
-<img width="700px" src="https://user-images.githubusercontent.com/116461/87863222-c1b76180-c90d-11ea-87d9-04bee1c58a0d.png" />
-
-## Managing your workspace
-
-Once you've opened/created the Foam repository, it will appear in the `Repositories` view of the `GistPad` tab (the one with the little notebook icon). From this tree view, you can add/edit/delete/rename new pages, upload local files, as well as view the backlinks for each page (they appear as child notes of a page).
-
-<img width="250px" src="https://user-images.githubusercontent.com/116461/87234704-83a7c400-c388-11ea-90a8-2a660bef4dc5.png" />
-
-## Editing your workspace
-
-When you create or open a page, you can edit the markdown content as usual, as well as [paste images](https://github.com/vsls-contrib/gistpad#pasting-images-1), and create [`[[links]]` to other pages](https://github.com/vsls-contrib/gistpad#links). When you type `[[`, you'll recieve auto-completion for the existing pages in your workspace, and you can also automatically create new pages by simply creating a link to it.
-
-Since you're using the Visual Studio Code markdown editor, you can benefit from all of the rich language services (e.g. syntax highlighting, header collapsing), as well as the extension ecosystem (e.g. [Emojisense](https://marketplace.visualstudio.com/items?itemName=bierner.emojisense)).
-
-## Navigating your workspace
-
-When editing a file, you can easily navigate `[[links]]` by hovering over them to see a preview of their contents and/or `cmd+clicking` on them in order to jump to the respective page. Furthermore, when you add a link to a page, a [backlink](https://github.com/vsls-contrib/gistpad#backlinks) is automatically added to it.
-
-You can view a page's backlinks using either of the following techniques:
-
-1. Expanding the file's node in the `Repositories` tree, since it's child nodes will represent backlinks. This makes it easy to browse your pages and their backlinks in a single hierachical view.
-
-1. Opening a file, and then viewing it's backlinks list at the bottom of the editor view. This makes it easy to read a page and then see its backlinks in a contextually rich way.
-
-## Daily Pages
-
-In addition to create arbitrary pages, you can also use GistPad for journaling or capturing [daily notes](https://github.com/vsls-contrib/gistpad#daily-pages). Simply click the calendar icon in the `Repositories` tree, which will open up the page that represents today. If the page doesn't already exist, then it will be created in the workspace before being opened.
-
-<img width="700px" src="https://user-images.githubusercontent.com/116461/87234721-b356cc00-c388-11ea-946a-e7f9c92258a6.png" />

docs/good-first-task.md

@@ -5,5 +5,5 @@ See the backlinks of this page for good first contribution opportunities.
 [[materialized-backlinks]] would help here.
 
 [//begin]: # "Autogenerated link references for markdown compatibility"
-[materialized-backlinks]: materialized-backlinks "Materialized Backlinks (stub)"
+[materialized-backlinks]: materialized-backlinks "Materialized Backlinks"
 [//end]: # "Autogenerated link references"

docs/graph-visualisation.md

@@ -6,4 +6,7 @@
 
 ![Demo of graph visualiser](assets/images/foam-navigation-demo.gif)
 
-
+[//begin]: # "Autogenerated link references for markdown compatibility"
+[wiki-links]: wiki-links "Wiki Links"
+[todo]: todo "Todo"
+[//end]: # "Autogenerated link references"

docs/images-from-your-clipboard.md

@@ -1,5 +1,5 @@
 # Images from your Clipboard
 
-You can directly link and paste images that are copied to the clipboard using either the [Paste
+You can directly link and paste images that are copied to the clipboard using the [Paste
 Image](https://marketplace.visualstudio.com/items?itemName=mushan.vscode-paste-image)
-extension, or the [Markdown Image](https://marketplace.visualstudio.com/items?itemName=hancel.markdown-image) extension. The former does not have MDX support (yet), the latter does.
+extension.

docs/inbox.md

@@ -11,10 +11,6 @@ Uncategorised thoughts, to be added
   - [Unotes](https://marketplace.visualstudio.com/items?itemName=ryanmcalister.Unotes)
   - [vscode-memo](https://github.com/svsool/vscode-memo)
   - [gistpad wiki](https://github.com/jevakallio/gistpad/tree/master/src/repos/wiki)
-- Open in Foam
-  - When you want to open a Foam published website in your own VS Code, we could have a "Open in Foam" link that opens the link in VS Code via a url binding (if possible), downloads the github repo locally, and opens it as a Foam workspace.
-  - Every Foam could have a different theme even in the editor, so you'll see it like they see it
-    - UI and layout design of your workspace can become a thing
 - Developer documentation
   - GistPad has a good vs code contrib primer: https://github.com/jevakallio/gistpad/blob/master/CONTRIBUTING.md  
 - VS Code Notebooks API

docs/index.md

@@ -62,7 +62,7 @@ These instructions assume you have a GitHub account, and you have Visual Studio
 
    <a class="github-button" href="https://github.com/foambubble/foam-template/generate" data-icon="octicon-repo-template" data-size="large" aria-label="Use this template foambubble/foam-template on GitHub">Use this template</a>
 
-   *If you want to keep your thoughts to yourself, remember to set the repository private, or if you don't want to use GitHub to host your workspace at all, choose [**Download as ZIP**](https://github.com/foambubble/foam-template/archive/master.zip) instead of **Use this template**.*
+   *If you want to keep your thoughts to yourself, remember to set the repository private, or if you don't want to use GitHub to host your workspace at all, choose **Download as ZIP** instead of **Use this template**.*
 
 2. [Clone the repository locally](https://help.github.com/en/github/creating-cloning-and-archiving-repositories/cloning-a-repository) and open it in VS Code.
 
@@ -139,16 +139,6 @@ If that sounds like something you're interested in, I'd love to have you along o
     <td align="center"><a href="https://github.com/nstafie"><img src="https://avatars1.githubusercontent.com/u/10801854?v=4" width="60px;" alt=""/><br /><sub><b>Nicholas Stafie</b></sub></a><br /><a href="https://github.com/foambubble/foam/commits?author=nstafie" title="Documentation">📖</a></td>
     <td align="center"><a href="https://github.com/francishamel"><img src="https://avatars3.githubusercontent.com/u/36383308?v=4" width="60px;" alt=""/><br /><sub><b>Francis Hamel</b></sub></a><br /><a href="https://github.com/foambubble/foam/commits?author=francishamel" title="Code">💻</a></td>
     <td align="center"><a href="http://digiguru.co.uk"><img src="https://avatars1.githubusercontent.com/u/619436?v=4" width="60px;" alt=""/><br /><sub><b>digiguru</b></sub></a><br /><a href="https://github.com/foambubble/foam/commits?author=digiguru" title="Code">💻</a> <a href="https://github.com/foambubble/foam/commits?author=digiguru" title="Documentation">📖</a></td>
-    <td align="center"><a href="https://github.com/chirag-singhal"><img src="https://avatars3.githubusercontent.com/u/42653703?v=4" width="60px;" alt=""/><br /><sub><b>CHIRAG SINGHAL</b></sub></a><br /><a href="https://github.com/foambubble/foam/commits?author=chirag-singhal" title="Code">💻</a></td>
-    <td align="center"><a href="https://github.com/lostintangent"><img src="https://avatars3.githubusercontent.com/u/116461?v=4" width="60px;" alt=""/><br /><sub><b>Jonathan Carter</b></sub></a><br /><a href="https://github.com/foambubble/foam/commits?author=lostintangent" title="Documentation">📖</a></td>
-    <td align="center"><a href="https://www.synesthesia.co.uk"><img src="https://avatars3.githubusercontent.com/u/181399?v=4" width="60px;" alt=""/><br /><sub><b>Julian Elve</b></sub></a><br /><a href="https://github.com/foambubble/foam/commits?author=synesthesia" title="Documentation">📖</a></td>
-  </tr>
-  <tr>
-    <td align="center"><a href="https://github.com/thomaskoppelaar"><img src="https://avatars3.githubusercontent.com/u/36331365?v=4" width="60px;" alt=""/><br /><sub><b>Thomas Koppelaar</b></sub></a><br /><a href="#question-thomaskoppelaar" title="Answering Questions">💬</a> <a href="https://github.com/foambubble/foam/commits?author=thomaskoppelaar" title="Code">💻</a> <a href="#userTesting-thomaskoppelaar" title="User Testing">📓</a></td>
-    <td align="center"><a href="http://www.akshaymehra.com"><img src="https://avatars1.githubusercontent.com/u/8671497?v=4" width="60px;" alt=""/><br /><sub><b>Akshay</b></sub></a><br /><a href="https://github.com/foambubble/foam/commits?author=MehraAkshay" title="Code">💻</a></td>
-    <td align="center"><a href="http://johnlindquist.com"><img src="https://avatars0.githubusercontent.com/u/36073?v=4" width="60px;" alt=""/><br /><sub><b>John Lindquist</b></sub></a><br /><a href="https://github.com/foambubble/foam/commits?author=johnlindquist" title="Documentation">📖</a></td>
-    <td align="center"><a href="https://ashwin.run/"><img src="https://avatars2.githubusercontent.com/u/1689183?v=4" width="60px;" alt=""/><br /><sub><b>Ashwin Ramaswami</b></sub></a><br /><a href="https://github.com/foambubble/foam/commits?author=epicfaace" title="Documentation">📖</a></td>
-    <td align="center"><a href="https://github.com/Klaudioz"><img src="https://avatars1.githubusercontent.com/u/632625?v=4" width="60px;" alt=""/><br /><sub><b>Claudio Canales</b></sub></a><br /><a href="https://github.com/foambubble/foam/commits?author=Klaudioz" title="Documentation">📖</a></td>
   </tr>
 </table>
 
@@ -165,6 +155,7 @@ If that sounds like something you're interested in, I'd love to have you along o
 Foam is licensed under the [MIT license](license).
 
 [//begin]: # "Autogenerated link references for markdown compatibility"
+[wiki-links]: wiki-links "Wiki Links"
 [graph-visualisation]: graph-visualisation "Graph visualisation"
 [backlinking]: backlinking "Backlinking"
 [recommended-extensions]: recommended-extensions "Recommended Extensions"

docs/link-formatting-and-autocompletion.md

@@ -1,75 +0,0 @@
-# Link Formatting and Autocompletion
-
-When coming from Roam, Obsidian and such tools, you may be used to writing [[wiki-links]] in `[[Title Case Format]]`. Foam will eventually support this syntax (see: [foambubble/rfcs#3](https://github.com/foambubble/rfcs/pull/3)), but for the time being, we do not.
-
-Foam relies heavily on our [[recommended-extensions]], and each extension has slightly different semantics and edge cases. This is a short guide on how to name your files, format your links, and configure your editor so that you can enjoy Foam until our implementation catches up with our aspirations.
-
-## Short version
-
-- Name your files in `lower-dash-case.md`. 
-  - Read on: [How to name your files](#how-to-name-your-files)
-- Use [[wiki-links]] that match the file name exactly, without file extension: `[[lower-dash-case]]`
-  - Read on: [How to format your links](#how-to-format-your-links)
-  - Read on: [How to autocomplete your links correctly](#how-to-autocomplete-your-links-correctly)
-- Ensure every file has a `# Heading` element
-  - This will be used as your document title.
-  
-## How to name your files
-
-As described in [[foam-file-format]], **Foam file names should not contain spaces.** Because of the [Markdown Notes](https://marketplace.visualstudio.com/items?itemName=kortina.vscode-markdown-notes) extension's default behaviour, we recommend naming your files in lower-dash-case: `foam-file-format.md`.
-
-ℹ️ This means:
-- All lowercase
-- No spaces, punctuation or special characters
-- Using dashes as word separators
-- Ending with a `.md` extension
-
-✅ Valid lower-dash-case file names include:
-- `roadmap.md`
-- `foam-file-format.md`
-- `f-f-f-f-falling.md`
-
-❌ Some invalid names include:
-
-- `Roadmap.md` (Name should not be capitalised)
-- `foam file format.md` (Name should not have spaces)
-- `f-f-f-f-falling!.md` (Name should not have special characters)
-
-Some of these file names may work for a subset of use cases (for example, if you don't publish your Foam site), but we'd still recommend following these rules.
-
-As per [[foam-file-format]], we eventually want to make Foam a lot more lenient. As per our [[principles]], you should be able to focus on your work and not fight against Foam. We're not there yet, but we'll get there.
-
-## How to format your links
-
-Use [[wiki-links]] to link between files. Each link:
-- **Should match file name exactly**: `[[foam-file-format]]`, not `[[Foam File Format]]`
-  - If you're reading this document on the Foam website, you might think: "That's not right!" What about links like [[foam-file-format]]! That uses spaces, capitalised letters, and everything!
-  - But if you look at the <a href="link-formatting-and-autocompletion.md">raw version of this document</a>, you'll see that the link is actually written as `[[foam-file-format]]`: we make it look nicer with a bit of web magic and a sprinkle of JavaScript.
-- **Not include a file extension**: `[[foam-file-format]]`, not `[[foam-file-format.md]]`.
-  - You might ask: If I can't use the `.md` extension, why does Foam autocomplete it for me?
-  - The answer is: It's a setting. See [How to autocomplete your links correctly](#how-to-autocomplete-your-links-correctly) below.
-
-## How to autocomplete your links correctly
-
-Foam autocompletion is provided by [Markdown Notes](https://marketplace.visualstudio.com/items?itemName=kortina.vscode-markdown-notes). The default behaviour of Markdown Notes Autocomplete is to suffix `.md` to the end of suggestion, such as in the below screenshot:
-
-![Autocomplete from Markdown Notes with file extension](./assets/images/md-notes-autocomplete-with-extension.png)
-
-To change this behaviour, add the below to your `.vscode/settings.json` file:
-
-```json
-"vscodeMarkdownNotes.noteCompletionConvention": "noExtension"
-```
-
-Now your autocomplete will look like the below screenshot:
-
-![Autocomplete from Markdown Notes without file extension](./assets/images/md-notes-autocomplete-no-extension.png)
-
-If you created your Foam from the official [foam-template](https://github.com/foambubble/foam-template) project after 27th July 2020, this setting should be already correctly set.
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[wiki-links]: wiki-links "Wiki Links"
-[recommended-extensions]: recommended-extensions "Recommended Extensions"
-[foam-file-format]: foam-file-format "Foam File Format"
-[principles]: principles "Principles"
-[//end]: # "Autogenerated link references"

docs/link-reference-definition-improvements.md

@@ -136,6 +136,7 @@ UI-wise, the publish targets could be picked in some similar fashion as the run/
 
 [//begin]: # "Autogenerated link references for markdown compatibility"
 [wiki-links]: wiki-links "Wiki Links"
+[roadmap]: roadmap "Roadmap"
 [link-reference-definitions]: link-reference-definitions "Link Reference Definitions"
 [backlinking]: backlinking "Backlinking"
 [//end]: # "Autogenerated link references"

docs/link-reference-definitions.md

@@ -24,50 +24,14 @@ The three components of a link reference definition are `[link-label]: link-targ
 
 - **link label:** The link text to match in the surrounding markdown document. This matches the inner bracket of the double-bracketed `[[wiki-link]]` notation
 - **link destination** The target of the matched link
-  - By default we generate links without extension. This can be overridden, see [Configuration](#configuration) below
+  - Right now we generate link destinations without file extension. This is a choice, see [discussion here](https://foambubble.github.io/foam/wiki-links#why-dont-wiki-links-work-on-github).
 - **"Link Title"** Optional title for link (The Foam template has a snippet of JavaScript to replace this on the website at runtime)
 
-## Configuration
-
-You can choose to generate link reference definitions with or without file extensions, depending on the target. As a rule of thumb:
-
-- Links with file extensions work better with standard markdown-based tools, such as GitHub web UI.
-- Links without file extensions work better with certain web publishing tools that treat links as literal urls and don't transform them automatically, such as the standard GitHub pages installation.
-
-By default, Foam generates links without file extensions for legacy reasons, but this may change in future versions. 
-
-You can override this setting in your Foam workspace's `settings.json`:
-
-- `"foam.edit.linkReferenceDefinitions": "withoutExtensions"` (default)
-- `"foam.edit.linkReferenceDefinitions": "withExtensions"`
-
-### Ignoring files
-
-Sometimes, you may want to ignore certain files or folders, so that Foam doesn't generate link reference definitions to them. 
-
-For instance, if you're using a local instance of [Jekyll](https://jekyllrb.com/), you may find that it writes copies of each `.md` file into a `_site` directory, which may lead to Foam generating references to them instead of the original source notes.
-
-You can ignore the `_site` directory by adding the following to your `.vscode/settings.json`:
-
-```json
-  "files.exclude": {
-    "**/_site": true
-  },
-  "files.watcherExclude": {
-    "**/_site": true
-  },
-```
-
-After changing the setting in your workspace, you can run the [[workspace-janitor]] command to convert all existing definitions. 
-
-[[Todo]] _Implement a `foam.eclude
-
-## Future improvements
-
 See [[link-reference-definition-improvements]] for further discussion on current problems and potential solutions.
 
 
 [//begin]: # "Autogenerated link references for markdown compatibility"
-[workspace-janitor]: workspace-janitor "Janitor"
+[wiki-links]: wiki-links "Wiki Links"
+[roadmap]: roadmap "Roadmap"
 [link-reference-definition-improvements]: link-reference-definition-improvements "Link Reference Definition Improvements"
-[//end]: # "Autogenerated link references"
+[//end]: # "Autogenerated link references"

docs/meeting-notes/foam-core-2020-07-11.md

@@ -123,5 +123,4 @@ How others solve this:
 
 [//begin]: # "Autogenerated link references for markdown compatibility"
 [todo]: ../todo "Todo"
-[Index]: ../index "Foam"
 [//end]: # "Autogenerated link references"

docs/mobile-apps.md

@@ -41,7 +41,9 @@ Given the effort vs reward ratio, it's a low priority for core team, but if some
 
 
 [//begin]: # "Autogenerated link references for markdown compatibility"
+[todo]: todo "Todo"
+[roadmap]: roadmap "Roadmap"
 [build-vs-assemble]: build-vs-assemble "Build vs Assemble"
 [wiki-links]: wiki-links "Wiki Links"
-[workspace-janitor]: workspace-janitor "Janitor"
+[workspace-janitor]: workspace-janitor "Workspace Janitor (stub)"
 [//end]: # "Autogenerated link references"

docs/new-note-for-testing.md

@@ -0,0 +1,4 @@
+
+[//begin]: # "Autogenerated link references for markdown compatibility"
+[unrelated]: unrelated "Unrelated"
+[//end]: # "Autogenerated link references"

docs/reading-list.md

@@ -6,7 +6,3 @@
 - [Dark mode](https://css-tricks.com/dark-modes-with-css/)
 
 
-
-[//begin]: # "Autogenerated link references for markdown compatibility"
-[Todo]: todo "Todo"
-[//end]: # "Autogenerated link references"

docs/recipes.md

@@ -33,9 +33,8 @@ Guides, tips and strategies for getting the most out of your Foam workspace!
 - Using [[backlinking]] for [[reference-lists]].
 
 ## Write
-- Link documents with [[wiki-links]], using Foam's [[link-formatting-and-autocompletion]].
+- Link documents with [[wiki-links]]
 - Use shortcuts for [[creating-new-notes]]
-- Instantly create and access your [[daily-notes]]
 - Draw [[diagrams-in-markdown]]
 - Prettify your links, [[automatically-expand-urls-to-well-titled-links]]
 - Style your environment with [[custom-markdown-preview-styles]]
@@ -50,8 +49,7 @@ Guides, tips and strategies for getting the most out of your Foam workspace!
 
 ## Version control
 
-- Quick commits with VS Code's built in [[git-integration]]
-- Store your workspace in an auto-synced GitHub repo with [[gistpad]]
+- Quick commits with [[git-integration]]
 - Sync your GitHub repo automatically [[todo]].
 
 ## Publish
@@ -59,7 +57,6 @@ Guides, tips and strategies for getting the most out of your Foam workspace!
 - Publish to [[github-pages]]
 - Publish to [[gitlab-pages]]
 - Publish your site with [[eleventy-and-netlify]]
-- Publish to [[azure-devops-wiki]]
 - Make the site your own by [[customising-styles]].
 - Math support [[math-support]]
 
@@ -71,7 +68,9 @@ Guides, tips and strategies for getting the most out of your Foam workspace!
 
 ## Workflow
 
-- Capture notes from Drafts app on iOS [[capture-notes-with-drafts-pro]]
+Workflow recipes wanted!
+
+_See [[contribution-guide]] and [[how-to-write-recipes]]._
 
 ## Creative ideas
 
@@ -96,21 +95,15 @@ _See [[contribution-guide]] and [[how-to-write-recipes]]._
 [unlinked-references]: unlinked-references "Unlinked references (stub)"
 [reference-lists]: reference-lists "Reference Lists"
 [wiki-links]: wiki-links "Wiki Links"
-[link-formatting-and-autocompletion]: link-formatting-and-autocompletion "Link Formatting and Autocompletion"
 [creating-new-notes]: creating-new-notes "Creating New Notes"
-[daily-notes]: daily-notes "Daily notes"
 [diagrams-in-markdown]: diagrams-in-markdown "Diagrams in Markdown"
 [automatically-expand-urls-to-well-titled-links]: automatically-expand-urls-to-well-titled-links "Automatically Expand URLs to Well-Titled Links"
 [custom-markdown-preview-styles]: custom-markdown-preview-styles "Custom Markdown Preview Styles"
 [images-from-your-clipboard]: images-from-your-clipboard "Images from your Clipboard"
 [good-first-task]: good-first-task "Good First Task"
 [git-integration]: git-integration "Git integration"
-[gistpad]: gistpad "GistPad"
 [github-pages]: github-pages "Github Pages"
-[gitlab-pages]: gitlab-pages "GitLab Pages"
 [eleventy-and-netlify]: eleventy-and-netlify "Eleventy and Netlify"
-[azure-devops-wiki]: azure-devops-wiki "Azure DevOps Wiki"
 [customising-styles]: customising-styles "Customising Styles"
 [math-support]: math-support "Math Support"
-[capture-notes-with-drafts-pro]: capture-notes-with-drafts-pro "Capture Notes With Drafts Pro"
 [//end]: # "Autogenerated link references"

docs/reference-lists.md

@@ -12,5 +12,5 @@ Use [[backlinking]] for handy reference lists:
 [//begin]: # "Autogenerated link references for markdown compatibility"
 [backlinking]: backlinking "Backlinking"
 [todo]: todo "Todo"
-[materialized-backlinks]: materialized-backlinks "Materialized Backlinks (stub)"
+[materialized-backlinks]: materialized-backlinks "Materialized Backlinks"
 [//end]: # "Autogenerated link references"

docs/referencing-notes-by-title.md

@@ -29,6 +29,6 @@
 - Can [MDX](https://github.com/mdx-js/mdx) help us here?
 
 [//begin]: # "Autogenerated link references for markdown compatibility"
-[unlinked-references]: unlinked-references "Unlinked references (stub)"
-[renaming-files]: renaming-files "Renaming files (stub)"
+[unlinked-references]: unlinked-references "Unlinked references"
+[renaming-files]: renaming-files "Renaming files"
 [//end]: # "Autogenerated link references"

docs/roadmap.md

@@ -35,6 +35,7 @@ If a roadmap item is a stub, **consider** opening a [GitHub issue](https://githu
 
 - [[renaming-files]]
 - [[unlinked-references]]
+- [[daily-notes]]
 - [[block-references]]
 - [[improved-backlinking]]
   - UX: [[make-backlinks-more-prominent]]
@@ -69,9 +70,8 @@ If a roadmap item is a stub, **consider** opening a [GitHub issue](https://githu
   - Discussion: [foam#55](https://github.com/foambubble/foam/issues/55)
 - [[migrating-from-obsidian]]
   - Discussion: [foam#46](https://github.com/foambubble/foam/issues/46)
-- [[Migrating from OneNote (stub)]]
-  - Discussion: [foam#151](https://github.com/foambubble/foam/issues/151)
 - _Migration from other tools..._
+
 ### integration
 - _Integrations to third party tools_...
   
@@ -84,7 +84,7 @@ If a roadmap item is a stub, **consider** opening a [GitHub issue](https://githu
 [build-vs-assemble]: build-vs-assemble "Build vs Assemble"
 [recipes]: recipes "Recipes"
 [cli]: cli "Command Line Interface"
-[workspace-janitor]: workspace-janitor "Janitor"
+[workspace-janitor]: workspace-janitor "Workspace Janitor"
 [contribution-guide]: contribution-guide "Contribution Guide"
 [improve-default-workspace-settings]: improve-default-workspace-settings "Improve Default Workspace Settings (stub)"
 [git-integration]: git-integration "Git integration"
@@ -92,14 +92,12 @@ If a roadmap item is a stub, **consider** opening a [GitHub issue](https://githu
 [foam-file-format]: foam-file-format "Foam File Format"
 [renaming-files]: renaming-files "Renaming files (stub)"
 [unlinked-references]: unlinked-references "Unlinked references (stub)"
+[daily-notes]: daily-notes "Daily notes"
 [block-references]: block-references "Block References (stub)"
 [improved-backlinking]: improved-backlinking "Improved Backlinking (stub)"
-[make-backlinks-more-prominent]: make-backlinks-more-prominent "Make Backlinks More Prominent"
 [materialized-backlinks]: materialized-backlinks "Materialized Backlinks (stub)"
 [automatic-git-syncing]: automatic-git-syncing "Automatic Git Syncing (stub)"
 [git-flows-for-teams]: git-flows-for-teams "Git Flows for Teams (stub)"
-[user-settings]: user-settings "User Settings (stub)"
-[link-reference-definitions]: link-reference-definitions "Link Reference Definitions"
 [officially-support-alternative-templates]: officially-support-alternative-templates "Officially Support Alternative Templates (stub)"
 [improved-static-site-generation]: improved-static-site-generation "Improved Static Site Generation (stub)"
 [mdx-by-default]: mdx-by-default "MDX by Default(stub)"
@@ -114,4 +112,5 @@ If a roadmap item is a stub, **consider** opening a [GitHub issue](https://githu
 [migrating-from-obsidian]: migrating-from-obsidian "Migrating from Obsidian (stub)"
 [foam-linter]: foam-linter "Foam Linter (stub)"
 [refactoring-via-language-server-protocol]: refactoring-via-language-server-protocol "Refactoring via Language Server Protocol (stub)"
-[//end]: # "Autogenerated link references"
+[make-backlinks-more-prominent]: make-backlinks-more-prominent "Make Backlinks More Prominent"
+[//end]: # "Autogenerated link references"

docs/wiki-links.md

@@ -2,9 +2,8 @@
 
 Foam enables you to Link pages together using `[[file-name]]` annotations (i.e. `[[media-wiki]]` links).
 
+- Both `[[file-name]]` and `[[file-name.md]]` work
 - Type `[[` and start typing a file name for autocompletion.
-  - Note that your file names should be in `lower-dash-case.md`, and your wiki links should reference file names exactly: `[[lower-dash-case]]`, not `[[Lower Dash Case]]`. 
-  - See [[link-formatting-and-autocompletion]] for more information, and how to setup your link autocompletions to make this easier.
 - `Cmd` + `Click` ( `Ctrl` + `Click` on Windows ) on file name to navigate to file (`F12` also works while your cursor is on the file name)
 - `Cmd` + `Click` ( `Ctrl` + `Click` on Windows ) on non-existent file to create that file in the workspace.
 
@@ -22,11 +21,9 @@ The [Foam for VSCode](https://marketplace.visualstudio.com/items?itemName=foam.f
 ## Read more
 
 - [[foam-file-format]]
-- [[link-formatting-and-autocompletion]]
 - See [[link-reference-definition-improvements]] for further discussion on current problems and potential solutions.
 
 [//begin]: # "Autogenerated link references for markdown compatibility"
-[link-formatting-and-autocompletion]: link-formatting-and-autocompletion "Link Formatting and Autocompletion"
 [link-reference-definitions]: link-reference-definitions "Link Reference Definitions"
 [foam-file-format]: foam-file-format "Foam File Format"
 [link-reference-definition-improvements]: link-reference-definition-improvements "Link Reference Definition Improvements"

docs/workspace-janitor.md

@@ -1,40 +1,69 @@
-# Janitor
+# Workspace Janitor
 
-To store your personal knowledge graph in markdown files instead of a database, we need some additional tooling to create and maintain relationships with notes.
+## What is it?
 
-**Foam Janitor** (inspired by Andy Matuschak's [note-link-janitor](https://github.com/andymatuschak/note-link-janitor)) helps you migrate existing notes to Foam, and maintain your Foam's health over time.
+To store your personal knowledge graph in markdown files instead of a database, we need some additional tooling to create and maintain:
 
-Currently, Foam's Janitor helps you to:
-- Ensure your [[link-reference-definitions]] are up to date
-- Ensure every document has a well-formatted title (required for Markdown Links, Markdown Notes, and Foam Gatsby Template compatibility)
+- Relationships between notes
+  - link references for [[wiki-links]]/markdown compatibility
+  - [[materialized-backlinks]]
+  - etc.
+- Format and structure of each note (e.g. title)
+- Renaming and refactoring files and directories
+- Linting related functionality
+  - File names
+  - Note links
+  - Zettelkasten linking
+- Visibility for orphaned notes
 
-In the future, Janitor can help you with
-- Updating [[materialized-backlinks]]
-- Lint, format and structure notes
-- Rename and move notes around while keeping their references up to date.
+This is necessary:
 
-## Using Janitor from VS Code (Experimental)
+- When migrating to Foam
+- To maintain your workspace health over long period of time
 
-Execute the "Foam: Run Janitor" command from the command palette.
+## Problem
 
-![Foam Janitor demo](assets/images/foam-janitor-demo.gif)
+Currently, the VS Code extension is very naive, and only updates the currently active editor. This isn't sufficient, because:
 
-## Using Janitor from command line (Experimental)
+- For e.g. [[materialized-backlinks]] to work, files need to update in the background.
+  - Separation of clean vs generated workspace for publishing?
+  - Support for standard markdown tools
+    - Output to a /build directory
+    - Would have to implement a custom previewer
+    - [[todo]] **Janne Ojanaho! Write a short proposal for this.**
+- If VS Code extension bugs our or is not ran, the workspace can lead in an inconsistent state
+- In collaboration scenarios, two people may change the same file, causing incomplete updates
+- If someone pushes changes from outside VS Code (Obsidian, Git Journal, etc.) links aren't updated
 
-> ⚠️ Improvements to this documentation are welcome!
+## Proposal
 
-The Janitor can be installed from [NPM](https://www.npmjs.com/) and executed as a standalone CLI tool:
+Implement a note janitor (working title, named after Andy Matuschak's [note-link-janitor](https://github.com/andymatuschak/note-link-janitor)), which ensures all files are correctly linked and updated, no matter how changes happen.
 
-```sh
-> npm install -g foam-cli
-> foam janitor path/to/workspace
-```
+Janitor should be runnable:
 
-You can run the Janitor as a git hook on every commit to ensure your workspace links are up to date. This can be especially helpful if you edit your markdown documents from other apps. 
+- From VS Code
+  - Replaces the existing logic in extension.ts
+  - In theory, we could do this using the [VS Code Tasks](https://code.visualstudio.com/docs/editor/tasks), exposing it from foam-vscode with a [TaskProvider](https://code.visualstudio.com/api/extension-guides/task-provider)
+  - It's not clear to me whether modifying the file in the active VS Code buffer from a background task is problematic for e.g. focus/selection management. I think this is how e.g. Prettier works, but not sure if there's some special case for the active editor.
+  - VS Code provides its own workspace watching functionality. Not sure it would be beneficial to use this over just chokidar-style file watching in the background
+- As a pre-push Git Hook (is this a good idea?) to ensure we send fully formed note graphs, even if you had to do some editing outside vs code
+- As a GitHub Action (for incoming changes via PRs and other apps like GitJournal)
+  - Run the "build" and push back to master/gh-pages
+- As a NPM script/dependency for any other purpose
 
-You can also run the Janitor from a GitHub action to ensure that all changes coming to your workspace are up to date. This can be useful when editing your Foam notes from mobile (i.e. via [GitJournal](https://gitjournal.io)), or your Foam has multiple contributors and you want to ensure that all changes are correctly integrated.
+## Software architecture
+
+- It's not really clear to me whether the workspace janitor should be its own package, or if the Janitor should just be the [[cli]] package, or the [[foam-core]] package.
+- Ideally the janitor should be lightweight so installing it on CI is quick
+- It would be cool if it didn't have many weird node-specific dependencies, maybe it could be even ran INSIDE a mobile application?
+- We don't want to pollute foam-core, but janitor might actually get quite diverse in use cases.
+
+Decoupling things like the core janitor API from the CLI API would help potentially with situations where we might want to have a separate file watcher strategy for CLI and active VS Code workspaces (see above).
 
 [//begin]: # "Autogenerated link references for markdown compatibility"
-[link-reference-definitions]: link-reference-definitions "Link Reference Definitions"
+[wiki-links]: wiki-links "Wiki Links"
 [materialized-backlinks]: materialized-backlinks "Materialized Backlinks (stub)"
+[cli]: cli "Command Line Interface"
+[foam-core]: foam-core "Foam Core"
+[todo]: todo "Todo"
 [//end]: # "Autogenerated link references"

lerna.json

@@ -4,5 +4,5 @@
   ],
   "npmClient": "yarn",
   "useWorkspaces": true,
-  "version": "0.3.1"
+  "version": "0.2.0"
 }

package.json

@@ -10,15 +10,7 @@
     "packages/*"
   ],
   "scripts": {
-    "watch:vscode": "yarn workspace foam-vscode watch",
-    "build:core": "yarn workspace foam-core build",
-    "watch:core": "yarn workspace foam-core start",
-    "test:core": "yarn workspace foam-core test",
-    "clean": "lerna run clean",
-    "build": "lerna run build",
-    "test": "lerna run test",
-    "lint": "lerna run lint",
-    "watch": "lerna run watch --concurrency 20 --stream"
+    "watch": "yarn workspace foam-vscode watch"
   },
   "devDependencies": {
     "all-contributors-cli": "^6.16.1",

packages/foam-cli/README.md

@@ -19,7 +19,7 @@ $ npm install -g foam-cli
 $ foam COMMAND
 running command...
 $ foam (-v|--version|version)
-foam-cli/0.3.0 darwin-x64 node-v12.18.0
+foam-cli/0.2.0 darwin-x64 node-v12.18.0
 $ foam --help [COMMAND]
 USAGE
   $ foam COMMAND
@@ -28,9 +28,28 @@ USAGE
 <!-- usagestop -->
 # Commands
 <!-- commands -->
+* [`foam hello [FILE]`](#foam-hello-file)
 * [`foam help [COMMAND]`](#foam-help-command)
-* [`foam janitor [WORKSPACEPATH]`](#foam-janitor-workspacepath)
-* [`foam migrate [WORKSPACEPATH]`](#foam-migrate-workspacepath)
+
+## `foam hello [FILE]`
+
+describe the command here
+
+```
+USAGE
+  $ foam hello [FILE]
+
+OPTIONS
+  -f, --force
+  -h, --help       show CLI help
+  -n, --name=name  name to print
+
+EXAMPLE
+  $ foam hello
+  hello world from ./src/hello.ts!
+```
+
+_See code: [src/commands/hello.ts](https://github.com/foambubble/foam/blob/v0.2.0/src/commands/hello.ts)_
 
 ## `foam help [COMMAND]`
 
@@ -48,43 +67,6 @@ OPTIONS
 ```
 
 _See code: [@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v3.1.0/src/commands/help.ts)_
-
-## `foam janitor [WORKSPACEPATH]`
-
-Updates link references and heading across all the markdown files in the given workspaces
-
-```
-USAGE
-  $ foam janitor [WORKSPACEPATH]
-
-OPTIONS
-  -h, --help                show CLI help
-  -w, --without-extensions  generate link reference definitions without extensions (for legacy support)
-
-EXAMPLE
-  $ foam-cli janitor path-to-foam-workspace
-```
-
-_See code: [src/commands/janitor.ts](https://github.com/foambubble/foam/blob/v0.3.0/src/commands/janitor.ts)_
-
-## `foam migrate [WORKSPACEPATH]`
-
-Updates file names, link references and heading across all the markdown files in the given workspaces
-
-```
-USAGE
-  $ foam migrate [WORKSPACEPATH]
-
-OPTIONS
-  -h, --help                show CLI help
-  -w, --without-extensions  generate link reference definitions without extensions (for legacy support)
-
-EXAMPLE
-  $ foam-cli migrate path-to-foam-workspace
-  Successfully generated link references and heading!
-```
-
-_See code: [src/commands/migrate.ts](https://github.com/foambubble/foam/blob/v0.3.0/src/commands/migrate.ts)_
 <!-- commandsstop -->
 
 ## Development

packages/foam-cli/package.json

@@ -1,7 +1,7 @@
 {
   "name": "foam-cli",
   "description": "Foam CLI",
-  "version": "0.3.0",
+  "version": "0.2.0",
   "author": "Jani Eväkallio @jevakallio",
   "bin": {
     "foam": "./bin/run"
@@ -11,7 +11,8 @@
     "@oclif/command": "^1",
     "@oclif/config": "^1",
     "@oclif/plugin-help": "^3",
-    "foam-core": "^0.3.0",
+    "chalk": "^4.1.0",
+    "foam-core": "^0.2.0",
     "ora": "^4.0.4",
     "tslib": "^1"
   },
@@ -26,6 +27,7 @@
     "eslint": "^5.13",
     "eslint-config-oclif": "^3.1",
     "eslint-config-oclif-typescript": "^0.1",
+    "foam-core": "^0.2.0",
     "globby": "^10",
     "jest": "^26.1.0",
     "mock-fs": "^4.12.0",
@@ -59,14 +61,12 @@
   },
   "repository": "foambubble/foam",
   "scripts": {
-    "clean": "rimraf tmp",
-    "build": "tsc -b",
-    "test": "jest",
-    "lint": "echo Missing lint task in CLI package",
     "cli": "./bin/run",
     "postpack": "rm -f oclif.manifest.json",
+    "posttest": "eslint . --ext .ts --config .eslintrc",
     "prepack": "rm -rf lib && tsc -b && oclif-dev manifest && oclif-dev readme",
+    "test": "jest",
     "version": "oclif-dev readme && git add README.md"
   },
   "types": "lib/index.d.ts"
-}
+}

packages/foam-cli/src/commands/hello.ts

@@ -0,0 +1,44 @@
+import {Command, flags} from '@oclif/command'
+import { NoteGraph } from 'foam-core';
+export default class Hello extends Command {
+  static description = 'describe the command here'
+
+  static examples = [
+    `$ foam hello
+hello world from ./src/hello.ts!
+`,
+  ]
+
+  static flags = {
+    help: flags.help({char: 'h'}),
+    // flag with a value (-n, --name=VALUE)
+    name: flags.string({char: 'n', description: 'name to print'}),
+    // flag with no value (-f, --force)
+    force: flags.boolean({char: 'f'}),
+  }
+
+  static args = [{name: 'file'}]
+
+  async run() {
+    const {args, flags} = this.parse(Hello)
+    const name = flags.name ?? 'world'
+
+//     const wm = new NoteGraph();
+//     wm.addNoteFromMarkdown('page-a.md', `
+// # Page A
+// ## Section
+// - [[page-b]]
+// - [[page-c]];
+//     `);
+
+//     wm.addNoteFromMarkdown('page-a.md', `
+// # Page B
+// This references [[page-a]]`);
+
+//     console.log(wm.getNoteWithLinks('page-a'));
+
+
+
+
+  }
+}

packages/foam-cli/src/commands/janitor.ts

@@ -1,37 +1,29 @@
 import { Command, flags } from '@oclif/command';
 import * as ora from 'ora';
-import {
-  initializeNoteGraph,
-  generateLinkReferences,
-  generateHeading,
-  applyTextEdit
-} from 'foam-core';
+import { initializeNoteGraph, generateLinkReferences, generateHeading, getKebabCaseFileName } from 'foam-core';
+import { applyTextEdit } from '../utils/apply-text-edit';
 import { writeFileToDisk } from '../utils/write-file-to-disk';
 import { isValidDirectory } from '../utils';
 
 export default class Janitor extends Command {
-  static description =
-    'Updates link references and heading across all the markdown files in the given workspaces';
+  static description = 'Updates link references and heading across all the markdown files in the given workspaces';
 
   static examples = [
     `$ foam-cli janitor path-to-foam-workspace
+Successfully generated link references and heading!
 `,
-  ];
+  ]
 
   static flags = {
-    'without-extensions': flags.boolean({
-      char: 'w',
-      description: 'generate link reference definitions without extensions (for legacy support)'
-    }),
     help: flags.help({ char: 'h' }),
-  };
+  }
 
-  static args = [{ name: 'workspacePath' }];
+  static args = [{ name: 'workspacePath' }]
 
   async run() {
     const spinner = ora('Reading Files').start();
 
-    const { args, flags } = this.parse(Janitor);
+    const { args, flags } = this.parse(Janitor)
 
     const { workspacePath = './' } = args;
 
@@ -44,7 +36,7 @@ export default class Janitor extends Command {
       spinner.text = `${notes.length} files found`;
       spinner.succeed();
 
-      // exit early if no files found.
+      // exit early if no files found. 
       if (notes.length === 0) {
         this.exit();
       }
@@ -54,25 +46,28 @@ export default class Janitor extends Command {
       const fileWritePromises = notes.map(note => {
         // Get edits
         const heading = generateHeading(note);
-        const definitions = generateLinkReferences(note, graph, !flags['without-extensions']);
+        const definitions = generateLinkReferences(note, graph);
+
 
         // apply Edits
         let file = note.source;
         file = heading ? applyTextEdit(file, heading) : file;
         file = definitions ? applyTextEdit(file, definitions) : file;
 
+
         if (heading || definitions) {
           return writeFileToDisk(note.path, file);
         }
 
-        return Promise.resolve(null);
-      });
+        return null;
+      })
 
       await Promise.all(fileWritePromises);
 
       spinner.succeed();
       spinner.succeed('Done!');
-    } else {
+    }
+    else {
       spinner.fail('Directory does not exist!');
     }
   }

packages/foam-cli/src/commands/lint.ts

@@ -0,0 +1,83 @@
+import { Command, flags } from '@oclif/command';
+import * as ora from 'ora';
+import * as chalk from 'chalk';
+import { initializeNoteGraph, Note, NoteLink } from 'foam-core';
+import * as fs from 'fs'
+
+interface InvalidReference {
+  note: Note,
+  link: NoteLink
+}
+
+export default class Lint extends Command {
+  static description = 'Shows lint errors and warnings across all the markdown files in the given workspaces';
+
+  // TODO: 
+  static examples = [
+    `$ foam-cli Lint path-to-foam-workspace
+Successfully generated link references and heading!
+`,
+  ]
+
+  static flags = {
+    help: flags.help({ char: 'h' }),
+  }
+
+  static args = [{ name: 'workspacePath' }]
+
+  async run() {
+    const spinner = ora('Reading Files').start();
+
+    const { args, flags } = this.parse(Lint)
+
+    const { workspacePath = './' } = args;
+
+
+    if (fs.existsSync(workspacePath) && fs.lstatSync(workspacePath).isDirectory()) {
+      const graph = await initializeNoteGraph(workspacePath);
+
+      const notes = graph.getNotes();
+
+      spinner.text = `${notes.length} files found`;
+
+
+
+      // TODO: Figure out why there is an undefined note
+      const orphanedNotes = notes.filter(note => note && graph.getBacklinks(note.id).length === 0);
+
+      // Find out invalid references
+      // ⚠️ Warning: Dirty code ahead. This is just a proof of concept.
+      // @ts-ignore
+      const invalidLinks: InvalidReference[] = notes.filter(Boolean).map(note => {
+        return graph
+          .getNoteLinks(note.id)
+          .map(link => {
+            const target = graph.getNote(link.to);
+            return !target ? { note: note, link: link } : false;
+          })
+          .filter(Boolean)
+      }).reduce((acc, curr) => ([...acc, ...curr]), []) // flatten the array
+
+      const warnings = `${orphanedNotes.map(note => {
+        return `→ "${note.title}" is an orphan note.`;
+      }).join('\n')}`;
+
+
+      const errors = `${invalidLinks.map(item => {
+        return `→ Link "${item.link.to}" in "${item.note.title}" points to a non-existing note [${item.link.position.start.line}, ${item.link.position.start.column}]   `;
+      }).join('\n')}`;
+
+
+      spinner.stop()
+
+      this.log(chalk.yellowBright('⚠️ Warnings:'));
+      this.log(warnings);
+
+      this.log(chalk.redBright('❌ Errors:'));
+      console.log(errors);
+    }
+    else {
+      spinner.fail('Directory does not exist!');
+    }
+  }
+}

packages/foam-cli/src/commands/migrate.ts

@@ -1,41 +1,31 @@
 import { Command, flags } from '@oclif/command';
 import * as ora from 'ora';
-import {
-  initializeNoteGraph,
-  generateLinkReferences,
-  generateHeading,
-  getKebabCaseFileName,
-  applyTextEdit
-} from 'foam-core';
+import { initializeNoteGraph, generateLinkReferences, generateHeading, getKebabCaseFileName } from 'foam-core';
+import { applyTextEdit } from '../utils/apply-text-edit';
 import { writeFileToDisk } from '../utils/write-file-to-disk';
 import { renameFile } from '../utils/rename-file';
 import { isValidDirectory } from '../utils';
 
 // @todo: Refactor 'migrate' and 'janitor' commands and avoid repeatition
 export default class Migrate extends Command {
-  static description =
-    'Updates file names, link references and heading across all the markdown files in the given workspaces';
+  static description = 'Updates file names, link references and heading across all the markdown files in the given workspaces';
 
   static examples = [
     `$ foam-cli migrate path-to-foam-workspace
 Successfully generated link references and heading!
 `,
-  ];
+  ]
 
   static flags = {
-    'without-extensions': flags.boolean({
-      char: 'w',
-      description: 'generate link reference definitions without extensions (for legacy support)'
-    }),
     help: flags.help({ char: 'h' }),
-  };
+  }
 
-  static args = [{ name: 'workspacePath' }];
+  static args = [{ name: 'workspacePath' }]
 
   async run() {
     const spinner = ora('Reading Files').start();
 
-    const { args, flags } = this.parse(Migrate);
+    const { args, flags } = this.parse(Migrate)
 
     const { workspacePath = './' } = args;
 
@@ -48,21 +38,19 @@ Successfully generated link references and heading!
       spinner.text = `${notes.length} files found`;
       spinner.succeed();
 
-      // exit early if no files found.
+      // exit early if no files found. 
       if (notes.length === 0) {
         this.exit();
       }
 
       // Kebab case file names
       const fileRename = notes.map(note => {
-        if (note.title != null) {
-          const kebabCasedFileName = getKebabCaseFileName(note.title);
-          if (kebabCasedFileName) {
-            return renameFile(note.path, kebabCasedFileName);
-          }
+        const kebabCasedFileName = getKebabCaseFileName(note.title);
+        if (kebabCasedFileName) {
+          return renameFile(note.path, kebabCasedFileName);
         }
-        return Promise.resolve(null);
-      });
+        return null;
+      })
 
       await Promise.all(fileRename);
 
@@ -74,32 +62,33 @@ Successfully generated link references and heading!
       notes = graph.getNotes().filter(Boolean); // remove undefined notes
 
       spinner.succeed();
-      spinner.text = 'Generating link definitions';
+      spinner.text = 'Generating link definitions'
 
-      const fileWritePromises = await Promise.all(
-        notes.map(note => {
-          // Get edits
-          const heading = generateHeading(note);
-          const definitions = generateLinkReferences(note, graph, !flags['without-extensions']);
+      const fileWritePromises = await Promise.all(notes.map(note => {
+        // Get edits
+        const heading = generateHeading(note);
+        const definitions = generateLinkReferences(note, graph);
 
-          // apply Edits
-          let file = note.source;
-          file = heading ? applyTextEdit(file, heading) : file;
-          file = definitions ? applyTextEdit(file, definitions) : file;
 
-          if (heading || definitions) {
-            return writeFileToDisk(note.path, file);
-          }
+        // apply Edits
+        let file = note.source;
+        file = heading ? applyTextEdit(file, heading) : file;
+        file = definitions ? applyTextEdit(file, definitions) : file;
 
-          return Promise.resolve(null);
-        })
-      );
+
+        if (heading || definitions) {
+          return writeFileToDisk(note.path, file);
+        }
+
+        return null;
+      }))
 
       await Promise.all(fileWritePromises);
 
       spinner.succeed();
       spinner.succeed('Done!');
-    } else {
+    }
+    else {
       spinner.fail('Directory does not exist!');
     }
   }

packages/foam-cli/src/utils/apply-text-edit.ts

@@ -1,9 +1,9 @@
-import { TextEdit } from '../index';
+import { TextEdit } from 'foam-core';
 
 /**
- *
+ * 
  * @param text text on which the textEdit will be applied
- * @param textEdit
+ * @param textEdit 
  * @returns {string} text with the applied textEdit
  */
 export const applyTextEdit = (text: string, textEdit: TextEdit): string => {
@@ -15,4 +15,4 @@ export const applyTextEdit = (text: string, textEdit: TextEdit): string => {
   const textToAppend = `${textEdit.newText}`;
   characters.splice(startOffset, deleteCount, textToAppend);
   return characters.join('');
-};
+} 

packages/foam-cli/src/utils/index.ts

@@ -1,4 +1,4 @@
 import * as fs from 'fs';
 
-export const isValidDirectory = (path: string) =>
-  fs.existsSync(path) && fs.lstatSync(path).isDirectory();
+
+export const isValidDirectory = (path: string) => fs.existsSync(path) && fs.lstatSync(path).isDirectory();

packages/foam-cli/src/utils/rename-file.ts

@@ -1,15 +1,9 @@
-import * as fs from 'fs';
-import * as path from 'path';
+import * as fs from 'fs'
 
-/**
- *
- * @param fileUri absolute path for the file that needs to renamed
- * @param newFileName  "new file name" without the extension
- */
 export const renameFile = async (fileUri: string, newFileName: string) => {
-  const dirName = path.dirname(fileUri);
-  const extension = path.extname(fileUri);
-  const newFileUri = path.join(dirName, `${newFileName}${extension}`);
+  const fileName = fileUri.split('/').pop();
+  const extension = fileName?.split('.').pop();
+  const newFileUri = fileUri.replace(`${fileName}`, `${newFileName}.${extension}`);
 
   return fs.promises.rename(fileUri, newFileUri);
-};
+}

packages/foam-cli/src/utils/write-file-to-disk.ts

@@ -1,5 +1,8 @@
 import * as fs from 'fs';
 
-export const writeFileToDisk = async (fileUri: string, data: string) => {
-  return fs.promises.writeFile(fileUri, data);
-};
+export const writeFileToDisk = async (fileUri: string, data: string): Promise<Boolean> => {
+  return fs.promises.writeFile(fileUri, data).then(() => true).catch(err => {
+    console.log('error while writing to file: ', err)
+    return false;
+  })
+}

packages/foam-cli/test/apply-text-edit.test.ts

@@ -1,12 +1,12 @@
-import { applyTextEdit } from '../../src/janitor/apply-text-edit';
+
+import { applyTextEdit } from '../src/utils/apply-text-edit';
 
 describe('applyTextEdit', () => {
   it('should return text with applied TextEdit in the end of the string', () => {
     const textEdit = {
       newText: `\n    4. this is fourth line`,
       range: {
-        start: { line: 3, column: 1, offset: 79 },
-        end: { line: 3, column: 1, offset: 79 },
+        start: { line: 3, column: 1, offset: 79 }, end: { line: 3, column: 1, offset: 79 },
       },
     };
 
@@ -23,17 +23,17 @@ describe('applyTextEdit', () => {
     4. this is fourth line
     `;
 
+
     const actual = applyTextEdit(text, textEdit);
 
-    expect(actual).toBe(expected);
-  });
+    expect(actual).toBe(expected)
+  })
 
   it('should return text with applied TextEdit at the top of the string', () => {
     const textEdit = {
       newText: `\n    1. this is first line`,
       range: {
-        start: { line: 0, column: 0, offset: 0 },
-        end: { line: 0, column: 0, offset: 0 },
+        start: { line: 0, column: 0, offset: 0 }, end: { line: 0, column: 0, offset: 0 },
       },
     };
 
@@ -48,17 +48,17 @@ describe('applyTextEdit', () => {
     3. this is third line
     `;
 
+
     const actual = applyTextEdit(text, textEdit);
 
-    expect(actual).toBe(expected);
+    expect(actual).toBe(expected)
   });
 
   it('should return text with applied TextEdit in the middle of the string', () => {
     const textEdit = {
       newText: `\n    2. this is the updated second line`,
       range: {
-        start: { line: 0, column: 0, offset: 26 },
-        end: { line: 0, column: 0, offset: 53 },
+        start: { line: 0, column: 0, offset: 26 }, end: { line: 0, column: 0, offset: 53 },
       },
     };
 
@@ -74,8 +74,9 @@ describe('applyTextEdit', () => {
     3. this is third line
     `;
 
+
     const actual = applyTextEdit(text, textEdit);
 
-    expect(actual).toBe(expected);
+    expect(actual).toBe(expected)
   });
-});
+})

packages/foam-cli/test/rename-file.test.ts

@@ -1,18 +1,14 @@
-import { renameFile } from '../src/utils/rename-file';
+
+import { renameFile } from '../src/utils/rename-file'
 import * as fs from 'fs';
 import mockFS from 'mock-fs';
 
-const doesFileExist = path =>
-  fs.promises
-    .access(path)
-    .then(() => true)
-    .catch(() => false);
-
 describe('renameFile', () => {
+
   const fileUri = './test/oldFileName.md';
 
   beforeAll(() => {
-    mockFS({ [fileUri]: '' });
+    mockFS({ [fileUri]: '' })
   });
 
   afterAll(() => {
@@ -20,11 +16,10 @@ describe('renameFile', () => {
   });
 
   it('should rename existing file', async () => {
-    expect(await doesFileExist(fileUri)).toBe(true);
-
+    expect(fs.existsSync(fileUri)).toBe(true);
     renameFile(fileUri, 'new-file-name');
 
-    expect(await doesFileExist(fileUri)).toBe(false);
-    expect(await doesFileExist('./test/new-file-name.md')).toBe(true);
+    expect(fs.existsSync(fileUri)).toBe(false);
+    expect(fs.existsSync('./test/new-file-name.md')).toBe(true);
   });
-});
+});

packages/foam-cli/test/write-file-to-disk.test.ts

@@ -1,4 +1,5 @@
-import { writeFileToDisk } from '../src/utils/write-file-to-disk';
+
+import { writeFileToDisk } from '../src/utils/write-file-to-disk'
 import * as fs from 'fs';
 import mockFS from 'mock-fs';
 
@@ -7,17 +8,17 @@ describe('writeFileToDisk', () => {
 
   beforeAll(() => {
     mockFS({ [fileUri]: 'content in the existing file' });
-  });
+  })
 
   afterAll(() => {
     fs.unlinkSync(fileUri);
     mockFS.restore();
-  });
+  })
 
   it('should overrwrite existing file in the disk with the new data', async () => {
     const expected = `content in the new file`;
     await writeFileToDisk(fileUri, expected);
-    const actual = await fs.promises.readFile(fileUri, { encoding: 'utf8' });
+    const actual = fs.readFileSync(fileUri, { encoding: 'utf8' });
     expect(actual).toBe(expected);
   });
-});
+})

packages/foam-core/package.json

@@ -2,17 +2,16 @@
   "name": "foam-core",
   "author": "Jani Eväkallio",
   "repository": "https://github.com/foambubble/foam",
-  "version": "0.3.0",
+  "version": "0.2.0",
   "license": "MIT",
   "files": [
     "dist"
   ],
   "scripts": {
-    "clean": "rimraf dist",
+    "start": "tsdx watch",
     "build": "tsdx build",
     "test": "tsdx test",
     "lint": "tsdx lint",
-    "watch": "tsdx watch",
     "prepare": "tsdx build"
   },
   "devDependencies": {

packages/foam-core/src/definitions.ts

@@ -1,2 +0,0 @@
-export const LINK_REFERENCE_DEFINITION_HEADER = `[//begin]: # "Autogenerated link references for markdown compatibility"`;
-export const LINK_REFERENCE_DEFINITION_FOOTER = `[//end]: # "Autogenerated link references"`;

packages/foam-core/src/index.ts

@@ -6,24 +6,12 @@ export {
   stringifyMarkdownLinkReferenceDefinition,
 } from './markdown-provider';
 
-export {
-  TextEdit,
-  generateHeading,
-  generateLinkReferences,
-  getKebabCaseFileName,
-} from './janitor';
+export { TextEdit, generateHeading, generateLinkReferences, getKebabCaseFileName } from './janitor'
 
-export { applyTextEdit } from './janitor/apply-text-edit';
-
-export { initializeNoteGraph } from './initialize-note-graph';
+export { initializeNoteGraph } from './initialize-note-graph'
 
 export { NoteGraph, Note, NoteLink };
 
-export {
-  LINK_REFERENCE_DEFINITION_HEADER,
-  LINK_REFERENCE_DEFINITION_FOOTER,
-} from './definitions';
-
 export interface FoamConfig {
   // TODO
 }

packages/foam-core/src/initialize-note-graph.ts

@@ -1,3 +1,4 @@
+
 import glob from 'glob';
 import { promisify } from 'util';
 import fs from 'fs';
@@ -10,8 +11,7 @@ const findAllFiles = promisify(glob);
 
 export const initializeNoteGraph = async (workspacePath: string) => {
   // remove trailing slash from workspacePath if exists
-  if (workspacePath.substr(-1) === '/')
-    workspacePath = workspacePath.slice(0, -1);
+  if (workspacePath.substr(-1) == '/') workspacePath = workspacePath.slice(0, -1);
 
   const files = await findAllFiles(`${workspacePath}/**/*.md`, {});
 
@@ -27,4 +27,4 @@ export const initializeNoteGraph = async (workspacePath: string) => {
   );
 
   return graph;
-};
+}

packages/foam-core/src/janitor/index.ts

@@ -1,47 +1,27 @@
 import { Position } from 'unist';
 import GithubSlugger from 'github-slugger';
-import {
-  Note,
-  NoteGraph,
-  LINK_REFERENCE_DEFINITION_HEADER,
-  LINK_REFERENCE_DEFINITION_FOOTER,
-} from '../index';
+import { Note, NoteGraph } from '../index';
 import {
   createMarkdownReferences,
   stringifyMarkdownLinkReferenceDefinition,
 } from '../markdown-provider';
-import { getHeadingFromFileName } from '../utils';
+import { getHeadingFromFileName } from '../utils'
 
-const slugger = new GithubSlugger();
+const slugger = new GithubSlugger()
 
 export interface TextEdit {
   range: Position;
   newText: string;
 }
 
-export const generateLinkReferences = (
-  note: Note,
-  ng: NoteGraph,
-  includeExtensions: boolean
-): TextEdit | null => {
+export const generateLinkReferences = (note: Note, ng: NoteGraph): TextEdit | null => {
   if (!note) {
     return null;
   }
 
-  const markdownReferences = createMarkdownReferences(
-    ng,
-    note.id,
-    includeExtensions
-  );
-
-  const newReferences =
-    markdownReferences.length === 0
-      ? ''
-      : [
-          LINK_REFERENCE_DEFINITION_HEADER,
-          ...markdownReferences.map(stringifyMarkdownLinkReferenceDefinition),
-          LINK_REFERENCE_DEFINITION_FOOTER,
-        ].join(note.eol);
+  const newReferences = createMarkdownReferences(ng, note.id).map(
+    stringifyMarkdownLinkReferenceDefinition
+  ).join('\n');
 
   if (note.definitions.length === 0) {
     if (newReferences.length === 0) {
@@ -60,11 +40,9 @@ export const generateLinkReferences = (
     const first = note.definitions[0];
     const last = note.definitions[note.definitions.length - 1];
 
-    const oldReferences = note.definitions
-      .map(stringifyMarkdownLinkReferenceDefinition)
-      .join(note.eol);
+    const oldRefrences = note.definitions.map(stringifyMarkdownLinkReferenceDefinition).join(note.eol);
 
-    if (oldReferences === newReferences) {
+    if (oldRefrences === newReferences) {
       return null;
     }
 
@@ -83,8 +61,8 @@ export const generateHeading = (note: Note): TextEdit | null => {
   if (!note) {
     return null;
   }
-
-  if (note.title) {
+  // Note: This may not work if the heading is same as the file name
+  if (note.title !== note.id) {
     return null;
   }
 
@@ -92,18 +70,18 @@ export const generateHeading = (note: Note): TextEdit | null => {
     newText: `# ${getHeadingFromFileName(note.id)}${note.eol}${note.eol}`,
     range: {
       start: { line: 0, column: 0, offset: 0 },
-      end: { line: 0, column: 0, offset: 0 },
-    },
-  };
+      end: { line: 0, column: 0, offset: 0 }
+    }
+  }
 };
 
 /**
- *
- * @param fileName
- * @returns null if file name is already in kebab case otherise returns
+ * 
+ * @param fileName 
+ * @returns null if file name is already in kebab case otherise returns 
  * the kebab cased file name
  */
 export const getKebabCaseFileName = (fileName: string) => {
   const kebabCasedFileName = slugger.slug(fileName);
   return kebabCasedFileName === fileName ? null : kebabCasedFileName;
-};
+}

packages/foam-core/src/markdown-provider.ts

@@ -2,7 +2,7 @@ import unified from 'unified';
 import markdownParse from 'remark-parse';
 import wikiLinkPlugin from 'remark-wiki-link';
 import visit, { CONTINUE, EXIT } from 'unist-util-visit';
-import { Node, Parent, Point } from 'unist';
+import { Node, Parent } from 'unist';
 import * as path from 'path';
 import { Note, NoteLink, NoteLinkDefinition, NoteGraph } from './note-graph';
 import { dropExtension } from './utils';
@@ -18,23 +18,19 @@ function parse(markdown: string): Node {
   return processor.parse(markdown);
 }
 
-export function createNoteFromMarkdown(
-  uri: string,
-  markdown: string,
-  eol: string
-): Note {
+export function createNoteFromMarkdown(uri: string, markdown: string, eol: string): Note {
   const filename = path.basename(uri);
   const id = path.parse(filename).name;
   const tree = parse(markdown);
-  let title: string | null = null;
+  let title = id;
   visit(tree, node => {
     if (node.type === 'heading' && node.depth === 1) {
       title = ((node as Parent)!.children[0].value as string) || title;
     }
-    return title === null ? CONTINUE : EXIT;
+    return title === id ? CONTINUE : EXIT;
   });
   const links: NoteLink[] = [];
-  const linkDefinitions: NoteLinkDefinition[] = [];
+  const definitions: NoteLinkDefinition[] = [];
   visit(tree, node => {
     if (node.type === 'wikiLink') {
       links.push({
@@ -45,7 +41,7 @@ export function createNoteFromMarkdown(
     }
 
     if (node.type === 'definition') {
-      linkDefinitions.push({
+      definitions.push({
         label: node.label as string,
         url: node.url as string,
         title: node.title as string,
@@ -55,36 +51,10 @@ export function createNoteFromMarkdown(
   });
 
   const end = tree.position!.end;
-  const definitions = getFoamDefinitions(linkDefinitions, end);
 
   return new Note(id, title, links, definitions, end, uri, markdown, eol);
 }
 
-function getFoamDefinitions(
-  defs: NoteLinkDefinition[],
-  fileEndPoint: Point
-): NoteLinkDefinition[] {
-  let previousLine = fileEndPoint.line;
-  let foamDefinitions = [];
-
-  // walk through each definition in reverse order
-  // (last one first)
-  for (const def of defs.reverse()) {
-    // if this definition is more than 2 lines above the
-    // previous one below it (or file end), that means we
-    // have exited the trailing definition block, and should bail
-    const start = def.position!.start.line;
-    if (start < previousLine - 2) {
-      break;
-    }
-
-    foamDefinitions.unshift(def);
-    previousLine = def.position!.end.line;
-  }
-
-  return foamDefinitions;
-}
-
 export function stringifyMarkdownLinkReferenceDefinition(
   definition: NoteLinkDefinition
 ) {
@@ -97,8 +67,7 @@ export function stringifyMarkdownLinkReferenceDefinition(
 }
 export function createMarkdownReferences(
   graph: NoteGraph,
-  noteId: string,
-  includeExtension: boolean
+  noteId: string
 ): NoteLinkDefinition[] {
   const source = graph.getNote(noteId);
 
@@ -129,16 +98,13 @@ export function createMarkdownReferences(
         path.dirname(source.path),
         target.path
       );
+      const relativePathWithoutExtension = dropExtension(relativePath);
 
-      const pathToNote = includeExtension
-        ? relativePath
-        : dropExtension(relativePath);
-
-      // [wiki-link-text]: path/to/file.md "Page title"
+      // [wiki-link-text]: wiki-link "Page title"
       return {
         label: link.text,
-        url: pathToNote,
-        title: target.title || target.id,
+        url: relativePathWithoutExtension,
+        title: target.title,
       };
     })
     .filter(Boolean)

packages/foam-core/src/note-graph.ts

@@ -1,7 +1,6 @@
 import { Graph, Edge } from 'graphlib';
 import { Position, Point } from 'unist';
 import GithubSlugger from 'github-slugger';
-import { EventEmitter } from 'events';
 
 type ID = string;
 
@@ -26,7 +25,7 @@ export interface NoteLinkDefinition {
 
 export class Note {
   public id: ID;
-  public title: string | null;
+  public title: string;
   public source: string;
   public path: string;
   public end: Point;
@@ -36,7 +35,7 @@ export class Note {
 
   constructor(
     id: ID,
-    title: string | null,
+    title: string,
     links: NoteLink[],
     definitions: NoteLinkDefinition[],
     end: Point,
@@ -55,32 +54,24 @@ export class Note {
   }
 }
 
-export type NoteGraphEventHandler = (e: { note: Note }) => void;
-
 export class NoteGraph {
   private graph: Graph;
-  private events: EventEmitter;
 
   constructor() {
     this.graph = new Graph();
-    this.events = new EventEmitter();
   }
 
   public setNote(note: Note) {
-    const noteExists = this.graph.hasNode(note.id);
-    if (noteExists) {
+    if (this.graph.hasNode(note.id)) {
       (this.graph.outEdges(note.id) || []).forEach(edge => {
         this.graph.removeEdge(edge);
       });
     }
-
     this.graph.setNode(note.id, note);
     note.links.forEach(link => {
       const slugger = new GithubSlugger();
       this.graph.setEdge(note.id, slugger.slug(link.to), link.text);
     });
-
-    this.events.emit(noteExists ? 'update' : 'add', { note });
   }
 
   public getNotes(): Note[] {
@@ -94,6 +85,13 @@ export class NoteGraph {
     throw new Error(`Note with ID [${noteId}] not found`);
   }
 
+  // Note: This is temporary until we figure out how to put 
+  // position inside Link (needed for linting)
+  public getNoteLinks(noteId: ID): NoteLink[] {
+    const note = this.getNote(noteId);
+    return note ? note.links : [];
+  }
+
   public getAllLinks(noteId: ID): Link[] {
     return (this.graph.nodeEdges(noteId) || []).map(edge =>
       convertEdgeToLink(edge, this.graph)
@@ -111,27 +109,10 @@ export class NoteGraph {
       convertEdgeToLink(edge, this.graph)
     );
   }
-
-  public unstable_onNoteAdded(callback: NoteGraphEventHandler) {
-    this.events.addListener('add', callback);
-  }
-
-  public unstable_onNoteUpdated(callback: NoteGraphEventHandler) {
-    this.events.addListener('update', callback);
-  }
-
-  public unstable_removeEventListener(callback: NoteGraphEventHandler) {
-    this.events.removeListener('add', callback);
-    this.events.removeListener('update', callback);
-  }
-
-  public dispose() {
-    this.events.removeAllListeners();
-  }
 }
 
 const convertEdgeToLink = (edge: Edge, graph: Graph): Link => ({
-  from: edge.v,
-  to: edge.w,
-  text: graph.edge(edge.v, edge.w),
+    from: edge.v,
+    to: edge.w,
+    text: graph.edge(edge.v, edge.w),
 });

packages/foam-core/src/utils.ts

@@ -7,10 +7,10 @@ export function dropExtension(path: string): string {
 }
 
 /**
- *
- * @param filename
+ * 
+ * @param filename 
  * @returns title cased heading after removing special characters
  */
 export const getHeadingFromFileName = (filename: string): string => {
   return titleCase(filename.replace(/[^\w\s]/gi, ' '));
-};
+}

packages/foam-core/test/__scaffold__/first-document.md

@@ -1,9 +1,5 @@
 # First Document
 
-Here's some [unrelated] content.
-
-[unrelated]: http://unrelated.com 'This link should not be changed'
-
 [[file-without-title]]
 
 [//begin]: # 'Autogenerated link references for markdown compatibility'

packages/foam-core/test/__scaffold__/third-document.md

@@ -6,7 +6,6 @@ All the link references are correct in this file.
 
 [[second-document]]
 
-[//begin]: # "Autogenerated link references for markdown compatibility"
+
 [first-document]: first-document "First Document"
-[second-document]: second-document "Second Document"
-[//end]: # "Autogenerated link references"
+[second-document]: second-document "Second Document"

packages/foam-core/test/janitor/generateHeadings.test.ts

@@ -12,6 +12,7 @@ describe('generateHeadings', () => {
 
   it('should add heading to a file that does not have them', () => {
     const note = _graph.getNote('file-without-title') as Note;
+
     const expected = {
       newText: `# File without Title
 
@@ -28,16 +29,17 @@ describe('generateHeadings', () => {
           offset: 0,
         },
       },
-    };
+    }
 
     const actual = generateHeading(note!);
 
     expect(actual!.range.start).toEqual(expected.range.start);
     expect(actual!.range.end).toEqual(expected.range.end);
     expect(actual!.newText).toEqual(expected.newText);
+
   });
 
-  it('should not cause any changes to a file that has a heading', () => {
+  it('should not cause any changes to a file that does heading', () => {
     const note = _graph.getNote('index') as Note;
 
     const expected = null;
@@ -45,5 +47,7 @@ describe('generateHeadings', () => {
     const actual = generateHeading(note!);
 
     expect(actual).toEqual(expected);
-  });
+
+  })
+
 });

packages/foam-core/test/janitor/generateLinkReferences.test.ts

@@ -18,11 +18,9 @@ describe('generateLinkReferences', () => {
     const note = _graph.getNote('index') as Note;
     const expected = {
       newText: `
-[//begin]: # "Autogenerated link references for markdown compatibility"
 [first-document]: first-document "First Document"
 [second-document]: second-document "Second Document"
-[file-without-title]: file-without-title "file-without-title"
-[//end]: # "Autogenerated link references"`,
+[file-without-title]: file-without-title "file-without-title"`,
       range: {
         start: {
           line: 10,
@@ -37,7 +35,7 @@ describe('generateLinkReferences', () => {
       },
     };
 
-    const actual = generateLinkReferences(note!, _graph, false);
+    const actual = generateLinkReferences(note!, _graph);
 
     expect(actual!.range.start).toEqual(expected.range.start);
     expect(actual!.range.end).toEqual(expected.range.end);
@@ -48,7 +46,7 @@ describe('generateLinkReferences', () => {
     const note = _graph.getNote('second-document') as Note;
 
     const expected = {
-      newText: '',
+      newText: "",
       range: {
         start: {
           line: 7,
@@ -63,7 +61,7 @@ describe('generateLinkReferences', () => {
       },
     };
 
-    const actual = generateLinkReferences(note!, _graph, false);
+    const actual = generateLinkReferences(note!, _graph);
 
     expect(actual!.range.start).toEqual(expected.range.start);
     expect(actual!.range.end).toEqual(expected.range.end);
@@ -74,24 +72,22 @@ describe('generateLinkReferences', () => {
     const note = _graph.getNote('first-document') as Note;
 
     const expected = {
-      newText: `[//begin]: # "Autogenerated link references for markdown compatibility"
-[file-without-title]: file-without-title "file-without-title"
-[//end]: # "Autogenerated link references"`,
+      newText: `[file-without-title]: file-without-title "file-without-title"`,
       range: {
         start: {
-          line: 9,
+          line: 5,
           column: 1,
-          offset: 145,
+          offset: 42,
         },
         end: {
-          line: 11,
+          line: 7,
           column: 43,
-          offset: 312,
+          offset: 209,
         },
       },
     };
 
-    const actual = generateLinkReferences(note!, _graph, false);
+    const actual = generateLinkReferences(note!, _graph);
 
     expect(actual!.range.start).toEqual(expected.range.start);
     expect(actual!.range.end).toEqual(expected.range.end);
@@ -103,7 +99,7 @@ describe('generateLinkReferences', () => {
 
     const expected = null;
 
-    const actual = generateLinkReferences(note!, _graph, false);
+    const actual = generateLinkReferences(note!, _graph);
 
     expect(actual).toEqual(expected);
   });

packages/foam-core/test/markdown-provider.test.ts

@@ -1,8 +1,5 @@
-import {
-  createNoteFromMarkdown,
-  createMarkdownReferences,
-} from '../src/markdown-provider';
-import { NoteGraph, Note } from '../src/note-graph';
+import { createNoteFromMarkdown } from '../src/markdown-provider';
+import { NoteGraph } from '../src/note-graph';
 
 const pageA = `
 # Page A
@@ -21,10 +18,7 @@ const pageC = `
 # Page C
 `;
 
-const pageD = `
-This file has no heading.
-`;
-
+// @todo: Add tests for definitions
 describe('Markdown loader', () => {
   it('Converts markdown to notes', () => {
     const graph = new NoteGraph();
@@ -55,65 +49,3 @@ describe('Markdown loader', () => {
     ]);
   });
 });
-
-describe('Note Title', () => {
-  it('should initialize note title if heading exists', () => {
-    const graph = new NoteGraph();
-    graph.setNote(createNoteFromMarkdown('page-a', pageA, '\n'));
-
-    const pageANoteTitle = (graph.getNote('page-a') as Note).title;
-    expect(pageANoteTitle).toBe('Page A');
-  });
-
-  it('should not initialize note title if heading does not exist', () => {
-    const graph = new NoteGraph();
-    graph.setNote(createNoteFromMarkdown('page-d', pageD, '\n'));
-
-    const pageANoteTitle = (graph.getNote('page-d') as Note).title;
-    expect(pageANoteTitle).toBe(null);
-  });
-});
-
-describe('wikilinks definitions', () => {
-  it('can generate links without file extension when includeExtension = false', () => {
-    const graph = new NoteGraph();
-    const noteA = createNoteFromMarkdown('dir1/page-a.md', pageA, '\n');
-    const noteB = createNoteFromMarkdown('dir1/page-b.md', pageB, '\n');
-    const noteC = createNoteFromMarkdown('dir1/page-c.md', pageC, '\n');
-    graph.setNote(noteA);
-    graph.setNote(noteB);
-    graph.setNote(noteC);
-
-    const noExtRefs = createMarkdownReferences(graph, noteA.id, false);
-    expect(noExtRefs.map(r => r.url)).toEqual(['page-b', 'page-c']);
-  });
-
-  it('can generate links with file extension when includeExtension = true', () => {
-    const graph = new NoteGraph();
-    const noteA = createNoteFromMarkdown('dir1/page-a.md', pageA, '\n');
-    const noteB = createNoteFromMarkdown('dir1/page-b.md', pageB, '\n');
-    const noteC = createNoteFromMarkdown('dir1/page-c.md', pageC, '\n');
-    graph.setNote(noteA);
-    graph.setNote(noteB);
-    graph.setNote(noteC);
-
-    const extRefs = createMarkdownReferences(graph, noteA.id, true);
-    expect(extRefs.map(r => r.url)).toEqual(['page-b.md', 'page-c.md']);
-  });
-
-  it('use relative paths', () => {
-    const graph = new NoteGraph();
-    const noteA = createNoteFromMarkdown('dir1/page-a.md', pageA, '\n');
-    const noteB = createNoteFromMarkdown('dir2/page-b.md', pageB, '\n');
-    const noteC = createNoteFromMarkdown('dir3/page-c.md', pageC, '\n');
-    graph.setNote(noteA);
-    graph.setNote(noteB);
-    graph.setNote(noteC);
-
-    const extRefs = createMarkdownReferences(graph, noteA.id, true);
-    expect(extRefs.map(r => r.url)).toEqual([
-      '../dir2/page-b.md',
-      '../dir3/page-c.md',
-    ]);
-  });
-});

packages/foam-vscode/CHANGELOG.md

@@ -4,24 +4,6 @@ All notable changes to the "foam-vscode" extension will be documented in this fi
 
 Check [Keep a Changelog](http://keepachangelog.com/) for recommendations on how to structure this file.
 
-## [0.3.1] - 2020-07-26
-
-Fixes and improvements:
-
-- Fix [Daily Notes](https://foambubble.github.io/foam/daily-notes) command on Windows.
-
-## [0.3.0] - 2020-07-25
-
-New features:
-
-- [Daily Notes](https://foambubble.github.io/foam/daily-notes) 
-- [Janitor](https://foambubble.github.io/foam/workspace-janitor) for updating headings and link references across your workspace
-
-Fixes and improvements: 
-
-- [Configuration setting for generating link reference definitions with file extension](https://foambubble.github.io/foam/link-reference-definitions#configuration) to support standard markdown tools, such as GitHub web UI
-- [Improvements to how new notes are indexed](https://github.com/foambubble/foam/pull/156)
-
 ## [0.2.0] - 2020-07-12
 
 Improvements:

packages/foam-vscode/package.json

@@ -4,7 +4,7 @@
   "description": "Generate markdown reference lists from wikilinks in a workspace",
   "author": "Jani Eväkallio",
   "repository": "https://github.com/foambubble/foam",
-  "version": "0.3.1",
+  "version": "0.2.0",
   "license": "MIT",
   "publisher": "foam",
   "engines": {
@@ -16,8 +16,7 @@
   "activationEvents": [
     "workspaceContains:.vscode/foam.json",
     "onCommand:foam-vscode.update-wikilinks",
-    "onCommand:foam-vscode.open-daily-note",
-    "onCommand:foam-vscode.janitor"
+    "onCommand:foam-vscode.open-daily-note"
   ],
   "main": "./out/extension.js",
   "contributes": {
@@ -29,27 +28,11 @@
       {
         "command": "foam-vscode.open-daily-note",
         "title": "Foam: Open Daily Note"
-      },
-      {
-        "command": "foam-vscode.janitor",
-        "title": "Foam: Run Janitor (Experimental)"
       }
     ],
     "configuration": {
       "title": "Foam",
       "properties": {
-        "foam.edit.linkReferenceDefinitions": {
-          "type": "string",
-          "default": "withoutExtensions",
-          "enum": [
-            "withExtensions",
-            "withoutExtensions"
-          ],
-          "enumDescriptions": [
-            "Include extension in wikilinks paths",
-            "Remove extension in wikilink paths"
-          ]
-        },
         "foam.openDailyNote.fileExtension": {
           "type": "string",
           "scope": "resource",
@@ -88,12 +71,10 @@
     ]
   },
   "scripts": {
-    "clean": "rimraf out",
-    "build": "tsc -p ./",
-    "test": "echo No tests in VSCode extensions yet",
+    "vscode:prepublish": "yarn npm-install && yarn run compile",
+    "compile": "tsc -p ./",
     "lint": "eslint src --ext ts",
     "watch": "tsc -watch -p ./",
-    "vscode:prepublish": "yarn npm-install && yarn run build",
     "npm-install": "rimraf node_modules && npm i",
     "npm-cleanup": "rimraf package-lock.json node_modules && yarn",
     "package-extension": "npx vsce package && yarn npm-cleanup",
@@ -114,6 +95,6 @@
   },
   "dependencies": {
     "dateformat": "^3.0.3",
-    "foam-core": "0.3.0"
+    "foam-core": "^0.2.0"
   }
 }

packages/foam-vscode/src/extension.ts

@@ -5,26 +5,11 @@
 "use strict";
 
 import * as fs from "fs";
-import {
-  workspace,
-  ExtensionContext,
-  window,
-  EndOfLine,
-  Uri,
-  FileSystemWatcher
-} from "vscode";
-
-import {
-  createNoteFromMarkdown,
-  createFoam,
-  FoamConfig,
-  Foam
-} from "foam-core";
+import { workspace, ExtensionContext, window, EndOfLine } from "vscode";
 
+import { createNoteFromMarkdown, createFoam, FoamConfig } from "foam-core";
 import { features } from "./features";
 
-let workspaceWatcher: FileSystemWatcher | null = null;
-
 export function activate(context: ExtensionContext) {
   const foamPromise = bootstrap(getConfig());
   features.forEach(f => {
@@ -32,55 +17,23 @@ export function activate(context: ExtensionContext) {
   });
 }
 
-export function deactivate() {
-  workspaceWatcher?.dispose();
-}
-
-function isLocalMarkdownFile(uri: Uri) {
-  return uri.scheme === "file" && uri.path.match(/\.(md|mdx|markdown)/i);
-}
-
-async function registerFile(foam: Foam, localUri: Uri) {
-  // read file from disk (async)
-  const path = localUri.fsPath;
-  const data = await fs.promises.readFile(path);
-  const markdown = (data || "").toString();
-
-  // create note
-  const eol =
-    window.activeTextEditor?.document?.eol === EndOfLine.CRLF ? "\r\n" : "\n";
-  const note = createNoteFromMarkdown(path, markdown, eol);
-
-  // add to graph
-  foam.notes.setNote(note);
-  return note;
-}
-
 const bootstrap = async (config: FoamConfig) => {
   const files = await workspace.findFiles("**/*");
   const foam = createFoam(config);
-  const addFile = (uri: Uri) => registerFile(foam, uri);
-
-  await Promise.all(files.filter(isLocalMarkdownFile).map(addFile));
-
-  workspaceWatcher = workspace.createFileSystemWatcher(
-    "**/*",
-    false,
-    true,
-    true
+  await Promise.all(
+    files
+      .filter(f => f.scheme === "file" && f.path.match(/\.(md|mdx|markdown)/i))
+      .map(f => {
+        return fs.promises.readFile(f.fsPath).then(data => {
+          const markdown = (data || "").toString();
+          const eol = window.activeTextEditor?.document?.eol === EndOfLine.CRLF ? "\r\n" : "\n";
+          foam.notes.setNote(createNoteFromMarkdown(f.fsPath, markdown, eol));
+        });
+      })
   );
-  
-  workspaceWatcher.onDidCreate(uri => {
-    if (isLocalMarkdownFile(uri)) {
-      addFile(uri).then(() => {
-        console.log(`Added ${uri} to workspace`);
-      });
-    }
-  });
-
   return foam;
 };
 
-export const getConfig = () => {
+const getConfig = () => {
   return {};
 };

packages/foam-vscode/src/features/index.ts

@@ -1,6 +1,5 @@
 import createReferences from "./wikilink-reference-generation";
 import openDailyNote from "./open-daily-note";
-import janitor from "./janitor";
 import { FoamFeature } from "../types";
 
-export const features: FoamFeature[] = [createReferences, openDailyNote, janitor];
+export const features: FoamFeature[] = [createReferences, openDailyNote];

packages/foam-vscode/src/features/janitor.ts

@@ -1,173 +0,0 @@
-import {
-  window,
-  workspace,
-  ExtensionContext,
-  commands,
-  Position,
-  Range
-} from "vscode";
-import fs = require("fs");
-import { FoamFeature } from "../types";
-import {
-  applyTextEdit,
-  generateLinkReferences,
-  generateHeading,
-  Foam,
-  Note
-} from "foam-core";
-
-import { includeExtensions } from "../settings";
-
-const feature: FoamFeature = {
-  activate: async (context: ExtensionContext, foamPromise: Promise<Foam>) => {
-    context.subscriptions.push(
-      commands.registerCommand("foam-vscode.janitor", async () =>
-        janitor(await foamPromise)
-      )
-    );
-  }
-};
-
-async function janitor(foam: Foam) {
-  try {
-    const outcome = await runJanitor(foam);
-    if (outcome.processedFileCount === 0) {
-      window.showInformationMessage(
-        "Foam Janitor didn't file any notes to clean up"
-      );
-    } else if (!outcome.changedAnyFiles) {
-      window.showInformationMessage(
-        `Foam Janitor checked ${outcome.processedFileCount} files, and found nothing to clean up!`
-      );
-    } else {
-      window.showInformationMessage(
-        `Foam Janitor checked ${outcome.processedFileCount} files and updated ${outcome.updatedDefinitionListCount} out-of-date definition lists and added ${outcome.updatedHeadingCount} missing headings. Please check the changes before committing them into version control!`
-      );
-    }
-  } catch (e) {
-    window.showErrorMessage(`Foam Janitor attempted to clean your workspace but ran into an error. Please check that we didn't break anything before committing any changes to version control, and pass the following error message to the Foam team on GitHub issues:
-    ${e.message}
-    ${e.stackTrace}`);
-  }
-}
-
-async function runJanitor(foam: Foam) {
-  const notes = foam.notes.getNotes().filter(Boolean);
-
-  let processedFileCount = 0;
-  let updatedHeadingCount = 0;
-  let updatedDefinitionListCount = 0;
-
-  const dirtyTextDocuments = workspace.textDocuments.filter(
-    textDocument =>
-      (textDocument.languageId === "markdown" ||
-        textDocument.languageId === "mdx") &&
-      textDocument.isDirty
-  );
-
-  const dirtyEditorsFileName = dirtyTextDocuments.map(
-    dirtyTextDocument => dirtyTextDocument.fileName
-  );
-
-  const dirtyNotes: Note[] = notes.filter(note =>
-    dirtyEditorsFileName.includes(note.path)
-  );
-
-  const nonDirtyNotes: Note[] = notes.filter(
-    note => !dirtyEditorsFileName.includes(note.path)
-  );
-
-  // Apply Text Edits to Non Dirty Notes using fs module just like CLI
-
-  const fileWritePromises = nonDirtyNotes.map(note => {
-    processedFileCount += 1;
-
-    let heading = generateHeading(note);
-    if (heading) {
-      console.log("fs.write heading " + note.path + " " + note.title);
-      updatedHeadingCount += 1;
-    }
-
-    let definitions = generateLinkReferences(
-      note,
-      foam.notes,
-      includeExtensions()
-    );
-    if (definitions) {
-      updatedDefinitionListCount += 1;
-    }
-
-    if (!heading && !definitions) {
-      return Promise.resolve();
-    }
-
-    // Apply Edits
-    // Note: The ordering matters. Definitions need to be inserted
-    // before heading, since inserting a heading changes line numbers below
-    let text = note.source;
-    text = definitions ? applyTextEdit(text, definitions) : text;
-    text = heading ? applyTextEdit(text, heading) : text;
-
-    return fs.promises.writeFile(note.path, text);
-  });
-
-  await Promise.all(fileWritePromises);
-
-  // Handle dirty editors in serial, as VSCode only allows
-  // edits to be applied to active text editors
-  for (const doc of dirtyTextDocuments) {
-    processedFileCount += 1;
-
-    const editor = await window.showTextDocument(doc);
-    const note = dirtyNotes.find(n => n.path === editor.document.fileName);
-
-    // Get edits
-    const heading = generateHeading(note);
-    let definitions = generateLinkReferences(
-      note,
-      foam.notes,
-      includeExtensions()
-    );
-
-    if (heading || definitions) {
-      // Apply Edits
-      await editor.edit(editBuilder => {
-        // Note: The ordering matters. Definitions need to be inserted
-        // before heading, since inserting a heading changes line numbers below
-        if (definitions) {
-          updatedDefinitionListCount += 1;
-          const start = new Position(
-            definitions.range.start.line - 1,
-            definitions.range.start.column
-          );
-          const end = new Position(
-            definitions.range.end.line - 1,
-            definitions.range.end.column
-          );
-          const range = new Range(start, end);
-          editBuilder.replace(range, definitions!.newText);
-        }
-
-        if (heading) {
-          console.log("editor.write heading " + note.title);
-
-          updatedHeadingCount += 1;
-          const start = new Position(
-            heading.range.start.line,
-            heading.range.start.column
-          );
-          editBuilder.insert(start, heading.newText);
-        }
-      });
-    }
-  }
-
-  return {
-    updatedHeadingCount,
-    updatedDefinitionListCount,
-    processedFileCount,
-    changedAnyFiles: updatedHeadingCount + updatedDefinitionListCount
-  };
-}
-
-export default feature;

packages/foam-vscode/src/features/open-daily-note.ts

@@ -5,13 +5,11 @@ import {
   WorkspaceConfiguration,
   ExtensionContext,
   commands,
-  Selection,
 } from "vscode";
 import { dirname, join } from "path";
 import dateFormat = require("dateformat");
 import fs = require("fs");
 import { FoamFeature } from "../types";
-import { docConfig } from '../utils';
 
 const feature: FoamFeature = {
   activate: async (context: ExtensionContext) => {
@@ -27,8 +25,8 @@ async function openDailyNote() {
 
   const dailyNotePath = getDailyNotePath(foamConfiguration, currentDate);
 
-  const isNew = await createDailyNoteIfNotExists(foamConfiguration, dailyNotePath, currentDate);
-  await focusDailyNote(dailyNotePath, isNew);
+  createDailyNoteIfNotExists(foamConfiguration, dailyNotePath, currentDate);
+  await focusDailyNote(dailyNotePath);
 }
 
 function getDailyNotePath(configuration: WorkspaceConfiguration, date: Date) {
@@ -58,9 +56,9 @@ async function createDailyNoteIfNotExists(
   configuration: WorkspaceConfiguration,
   dailyNotePath: string,
   currentDate: Date
- ) {
+) {
   if (await pathExists(dailyNotePath)) {
-    return false;
+    return;
   }
 
   createDailyNoteDirectoryIfNotExists(dailyNotePath);
@@ -71,10 +69,8 @@ async function createDailyNoteIfNotExists(
 
   await fs.promises.writeFile(
     dailyNotePath,
-    `# ${dateFormat(currentDate, titleFormat, false)}${docConfig.eol}${docConfig.eol}`
+    `# ${dateFormat(currentDate, titleFormat, false)}\r\n`
   );
-
-  return true;
 }
 
 async function createDailyNoteDirectoryIfNotExists(dailyNotePath: string) {
@@ -85,16 +81,9 @@ async function createDailyNoteDirectoryIfNotExists(dailyNotePath: string) {
   }
 }
 
-async function focusDailyNote(dailyNotePath: string, isNewNote: boolean) {
-  const document = await workspace.openTextDocument(Uri.file(dailyNotePath));
-  const editor = await window.showTextDocument(document);
-
-  // Move the cursor to end of the file
-  if (isNewNote) {
-    const { lineCount } = editor.document;
-    const { range } = editor.document.lineAt(lineCount - 1);
-    editor.selection = new Selection(range.end, range.end);
-  }
+async function focusDailyNote(dailyNotePath: string) {
+  const document = await workspace.openTextDocument(Uri.parse(dailyNotePath));
+  window.showTextDocument(document);
 }
 
 async function pathExists(path: string) {

packages/foam-vscode/src/features/wikilink-reference-generation.ts

@@ -18,9 +18,7 @@ import {
   stringifyMarkdownLinkReferenceDefinition,
   createNoteFromMarkdown,
   NoteGraph,
-  Foam,
-  LINK_REFERENCE_DEFINITION_HEADER,
-  LINK_REFERENCE_DEFINITION_FOOTER
+  Foam
 } from "foam-core";
 import { basename } from "path";
 import {
@@ -33,20 +31,19 @@ import {
   dropExtension
 } from "../utils";
 import { FoamFeature } from "../types";
-import { includeExtensions } from "../settings";
 
 const feature: FoamFeature = {
   activate: async (context: ExtensionContext, foamPromise: Promise<Foam>) => {
     const foam = await foamPromise;
-
     context.subscriptions.push(
       commands.registerCommand("foam-vscode.update-wikilinks", () =>
         updateReferenceList(foam.notes)
       ),
-
       workspace.onWillSaveTextDocument(e => {
         if (e.document.languageId === "markdown") {
-          updateDocumentInNoteGraph(foam, e.document);
+          foam.notes.setNote(
+            createNoteFromMarkdown(e.document.fileName, e.document.getText(), docConfig.eol)
+          );
           e.waitUntil(updateReferenceList(foam.notes));
         }
       }),
@@ -55,30 +52,14 @@ const feature: FoamFeature = {
         new WikilinkReferenceCodeLensProvider(foam.notes)
       )
     );
-
-    // when a file is created as a result of peekDefinition
-    // action on a wikilink, add definition update references
-    foam.notes.unstable_onNoteAdded(e => {
-      let editor = window.activeTextEditor;
-      if (!editor || !isMdEditor(editor)) {
-        return;
-      }
-
-      updateDocumentInNoteGraph(foam, editor.document);
-      updateReferenceList(foam.notes);
-    });
   }
 };
 
-function updateDocumentInNoteGraph(foam: Foam, document: TextDocument) {
-  foam.notes.setNote(
-    createNoteFromMarkdown(document.fileName, document.getText(), docConfig.eol)
-  );
-}
+const REFERENCE_HEADER = `[//begin]: # "Autogenerated link references for markdown compatibility"`;
+const REFERENCE_FOOTER = `[//end]: # "Autogenerated link references"`;
 
 async function createReferenceList(foam: NoteGraph) {
   let editor = window.activeTextEditor;
-
   if (!editor || !isMdEditor(editor)) {
     return;
   }
@@ -128,7 +109,6 @@ async function updateReferenceList(foam: NoteGraph) {
   }
 }
 
-
 async function generateReferenceList(
   foam: NoteGraph,
   doc: TextDocument
@@ -138,17 +118,13 @@ async function generateReferenceList(
   const id = dropExtension(basename(filePath));
 
   const references = uniq(
-    createMarkdownReferences(foam, id, includeExtensions()).map(
+    createMarkdownReferences(foam, id).map(
       stringifyMarkdownLinkReferenceDefinition
     )
   );
 
   if (references.length) {
-    return [
-      LINK_REFERENCE_DEFINITION_HEADER,
-      ...references,
-      LINK_REFERENCE_DEFINITION_FOOTER
-    ];
+    return [REFERENCE_HEADER, ...references, REFERENCE_FOOTER];
   }
 
   return [];
@@ -161,8 +137,8 @@ async function generateReferenceList(
 function detectReferenceListRange(doc: TextDocument): Range {
   const fullText = doc.getText();
 
-  const headerIndex = fullText.indexOf(LINK_REFERENCE_DEFINITION_HEADER);
-  const footerIndex = fullText.lastIndexOf(LINK_REFERENCE_DEFINITION_FOOTER);
+  const headerIndex = fullText.indexOf(REFERENCE_HEADER);
+  const footerIndex = fullText.lastIndexOf(REFERENCE_FOOTER);
 
   if (headerIndex < 0) {
     return null;
@@ -180,7 +156,7 @@ function detectReferenceListRange(doc: TextDocument): Range {
 
   return new Range(
     new Position(headerLine, 0),
-    new Position(footerLine, LINK_REFERENCE_DEFINITION_FOOTER.length)
+    new Position(footerLine, REFERENCE_FOOTER.length)
   );
 }
 

packages/foam-vscode/src/settings.ts

@@ -1,18 +0,0 @@
-import { workspace } from 'vscode';
-
-export enum LinkReferenceDefinitionsSetting {
-  withExtensions = "withExtensions",
-  withoutExtensions = "withoutExtensions"
-};
-
-export function includeExtensions() {
-  const linkDefinitionSetting: LinkReferenceDefinitionsSetting =
-  workspace
-    .getConfiguration("foam.edit")
-    .get<LinkReferenceDefinitionsSetting>("linkReferenceDefinitions") ??
-  LinkReferenceDefinitionsSetting.withoutExtensions;
-
-  return linkDefinitionSetting === LinkReferenceDefinitionsSetting.withExtensions;
-}
-
-  

readme.md

@@ -7,7 +7,7 @@
 # Foam
 
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-33-orange.svg?style=flat-square)](#contributors-)
+[![All Contributors](https://img.shields.io/badge/all_contributors-25-orange.svg?style=flat-square)](#contributors-)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 **Foam** is a personal knowledge management and sharing system inspired by [Roam Research](https://roamresearch.com/), built on [Visual Studio Code](https://code.visualstudio.com/) and [GitHub](https://github.com/).
@@ -20,7 +20,7 @@ You can use **Foam** for organising your research, keeping re-discoverable notes
 
 Whether you want to build a [Second Brain](https://www.buildingasecondbrain.com/) or a [Zettelkasten](https://zettelkasten.de/posts/overview/), write a book, or just get better at long-term learning, **Foam** can help you organise your thoughts if you follow these simple rules:
 
-1. Create a single **Foam** workspace for all your knowledge and research following the [Getting started](https://foambubble.github.io/foam#getting-started) guide.
+1. Create a single **Foam** workspace for all your knowledge and research following the [Getting started](https://foambubble.github.io/foam#getting-started) guide .
 2. Write your thoughts in markdown documents (I like to call them **Bubbles**, but that might be more than a little twee). These documents should be atomic: Put things that belong together into a single document, and limit its content to that single topic. ([source](https://zettelkasten.de/posts/overview/#principles))
 3. Use Foam's shortcuts and autocompletions to link your thoughts together with `[[wiki-links]]`, and navigate between them to explore your knowledge graph.
 4. Get an overview of your **Foam** workspace using the [[Graph Visualisation](https://foambubble.github.io/foam/graph-visualisation)], and discover relationships between your thoughts with the use of [[Backlinking](https://foambubble.github.io/foam/backlinking)].
@@ -89,16 +89,6 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
     <td align="center"><a href="https://github.com/nstafie"><img src="https://avatars1.githubusercontent.com/u/10801854?v=4" width="60px;" alt=""/><br /><sub><b>Nicholas Stafie</b></sub></a><br /><a href="https://github.com/foambubble/foam/commits?author=nstafie" title="Documentation">📖</a></td>
     <td align="center"><a href="https://github.com/francishamel"><img src="https://avatars3.githubusercontent.com/u/36383308?v=4" width="60px;" alt=""/><br /><sub><b>Francis Hamel</b></sub></a><br /><a href="https://github.com/foambubble/foam/commits?author=francishamel" title="Code">💻</a></td>
     <td align="center"><a href="http://digiguru.co.uk"><img src="https://avatars1.githubusercontent.com/u/619436?v=4" width="60px;" alt=""/><br /><sub><b>digiguru</b></sub></a><br /><a href="https://github.com/foambubble/foam/commits?author=digiguru" title="Code">💻</a> <a href="https://github.com/foambubble/foam/commits?author=digiguru" title="Documentation">📖</a></td>
-    <td align="center"><a href="https://github.com/chirag-singhal"><img src="https://avatars3.githubusercontent.com/u/42653703?v=4" width="60px;" alt=""/><br /><sub><b>CHIRAG SINGHAL</b></sub></a><br /><a href="https://github.com/foambubble/foam/commits?author=chirag-singhal" title="Code">💻</a></td>
-    <td align="center"><a href="https://github.com/lostintangent"><img src="https://avatars3.githubusercontent.com/u/116461?v=4" width="60px;" alt=""/><br /><sub><b>Jonathan Carter</b></sub></a><br /><a href="https://github.com/foambubble/foam/commits?author=lostintangent" title="Documentation">📖</a></td>
-    <td align="center"><a href="https://www.synesthesia.co.uk"><img src="https://avatars3.githubusercontent.com/u/181399?v=4" width="60px;" alt=""/><br /><sub><b>Julian Elve</b></sub></a><br /><a href="https://github.com/foambubble/foam/commits?author=synesthesia" title="Documentation">📖</a></td>
-  </tr>
-  <tr>
-    <td align="center"><a href="https://github.com/thomaskoppelaar"><img src="https://avatars3.githubusercontent.com/u/36331365?v=4" width="60px;" alt=""/><br /><sub><b>Thomas Koppelaar</b></sub></a><br /><a href="#question-thomaskoppelaar" title="Answering Questions">💬</a> <a href="https://github.com/foambubble/foam/commits?author=thomaskoppelaar" title="Code">💻</a> <a href="#userTesting-thomaskoppelaar" title="User Testing">📓</a></td>
-    <td align="center"><a href="http://www.akshaymehra.com"><img src="https://avatars1.githubusercontent.com/u/8671497?v=4" width="60px;" alt=""/><br /><sub><b>Akshay</b></sub></a><br /><a href="https://github.com/foambubble/foam/commits?author=MehraAkshay" title="Code">💻</a></td>
-    <td align="center"><a href="http://johnlindquist.com"><img src="https://avatars0.githubusercontent.com/u/36073?v=4" width="60px;" alt=""/><br /><sub><b>John Lindquist</b></sub></a><br /><a href="https://github.com/foambubble/foam/commits?author=johnlindquist" title="Documentation">📖</a></td>
-    <td align="center"><a href="https://ashwin.run/"><img src="https://avatars2.githubusercontent.com/u/1689183?v=4" width="60px;" alt=""/><br /><sub><b>Ashwin Ramaswami</b></sub></a><br /><a href="https://github.com/foambubble/foam/commits?author=epicfaace" title="Documentation">📖</a></td>
-    <td align="center"><a href="https://github.com/Klaudioz"><img src="https://avatars1.githubusercontent.com/u/632625?v=4" width="60px;" alt=""/><br /><sub><b>Claudio Canales</b></sub></a><br /><a href="https://github.com/foambubble/foam/commits?author=Klaudioz" title="Documentation">📖</a></td>
   </tr>
 </table>
 
@@ -106,4 +96,4 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
 <!-- prettier-ignore-end -->
 <!-- ALL-CONTRIBUTORS-LIST:END -->
 
-This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!
+This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!

yarn.lock

@@ -5188,22 +5188,6 @@ flush-write-stream@^1.0.0:
     inherits "^2.0.3"
     readable-stream "^2.3.6"
 
-foam-core@0.3.0-alpha.0:
-  version "0.3.0-alpha.0"
-  resolved "https://registry.yarnpkg.com/foam-core/-/foam-core-0.3.0-alpha.0.tgz#792ef6b344854f6e34af954cbbce0a39c1657712"
-  integrity sha512-HNCjlb8LtWePry/llLQRm5L8pJGredD6bj3WrILivIwIvYiXhhNzuIdFZkkUQKLcxQawKGBs9SkIapYrAk0rFw==
-  dependencies:
-    detect-newline "^3.1.0"
-    github-slugger "^1.3.0"
-    glob "^7.1.6"
-    graphlib "^2.1.8"
-    lodash "^4.17.19"
-    remark-parse "^8.0.2"
-    remark-wiki-link "^0.0.4"
-    title-case "^3.0.2"
-    unified "^9.0.0"
-    unist-util-visit "^2.0.2"
-
 for-in@^1.0.2:
   version "1.0.2"
   resolved "https://registry.yarnpkg.com/for-in/-/for-in-1.0.2.tgz#81068d295a8142ec0ac726c6e2200c30fb6d5e80"