From 2fa2feacafa95a82e363e8b036f2ad95f08d5227 Mon Sep 17 00:00:00 2001
From: Wliu <50Wliu@users.noreply.github.com>
Date: Wed, 9 Aug 2017 22:52:39 -0400
Subject: [PATCH 1/3] Multiline is important, don't forget to set it

---
 src/workspace.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/workspace.js b/src/workspace.js
index 3bf112461..ad37630eb 100644
--- a/src/workspace.js
+++ b/src/workspace.js
@@ -1949,7 +1949,7 @@ module.exports = class Workspace extends Model {
       }
 
       if (!outOfProcessFinished.length) {
-        let flags = 'g'
+        let flags = 'gm' // set multiline flag so ^ and $ match start/end of line, not file
         if (regex.ignoreCase) { flags += 'i' }
 
         const task = Task.once(

From 95b216f2345589aa36ea6801babb27bd6526a226 Mon Sep 17 00:00:00 2001
From: Wliu <50Wliu@users.noreply.github.com>
Date: Wed, 9 Aug 2017 23:15:33 -0400
Subject: [PATCH 2/3] Add multiline spec

---
 spec/workspace-spec.js | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/spec/workspace-spec.js b/spec/workspace-spec.js
index bdd5677c8..add555f28 100644
--- a/spec/workspace-spec.js
+++ b/spec/workspace-spec.js
@@ -2394,6 +2394,22 @@ i = /test/; #FIXME\
           expect(results[0].replacements).toBe(6)
         })
       })
+
+      it('uses the multiline flag when searching', () => {
+        const filePath = path.join(projectDir, 'sample.js')
+        fs.copyFileSync(path.join(fixturesDir, 'sample.js'), filePath)
+
+        const results = []
+        waitsForPromise(() =>
+          atom.workspace.replace(/;$/gi, 'items', [filePath], result => results.push(result))
+        )
+
+        runs(() => {
+          expect(results).toHaveLength(1)
+          expect(results[0].filePath).toBe(filePath)
+          expect(results[0].replacements).toBe(8)
+        })
+      })
     })
 
     describe('when a buffer is already open', () => {

From 8963cf495517bddf197441f54deb112167d8b209 Mon Sep 17 00:00:00 2001
From: Wliu <50Wliu@users.noreply.github.com>
Date: Thu, 10 Aug 2017 13:24:46 -0400
Subject: [PATCH 3/3] Only use multiline if the flag is passed in

---
 spec/workspace-spec.js | 4 ++--
 src/workspace.js       | 3 ++-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/spec/workspace-spec.js b/spec/workspace-spec.js
index add555f28..476a4ba5b 100644
--- a/spec/workspace-spec.js
+++ b/spec/workspace-spec.js
@@ -2395,13 +2395,13 @@ i = /test/; #FIXME\
         })
       })
 
-      it('uses the multiline flag when searching', () => {
+      it('does not discard the multiline flag', () => {
         const filePath = path.join(projectDir, 'sample.js')
         fs.copyFileSync(path.join(fixturesDir, 'sample.js'), filePath)
 
         const results = []
         waitsForPromise(() =>
-          atom.workspace.replace(/;$/gi, 'items', [filePath], result => results.push(result))
+          atom.workspace.replace(/;$/gmi, 'items', [filePath], result => results.push(result))
         )
 
         runs(() => {
diff --git a/src/workspace.js b/src/workspace.js
index ad37630eb..17c6b2a8b 100644
--- a/src/workspace.js
+++ b/src/workspace.js
@@ -1949,7 +1949,8 @@ module.exports = class Workspace extends Model {
       }
 
       if (!outOfProcessFinished.length) {
-        let flags = 'gm' // set multiline flag so ^ and $ match start/end of line, not file
+        let flags = 'g'
+        if (regex.multiline) { flags += 'm' }
         if (regex.ignoreCase) { flags += 'i' }
 
         const task = Task.once(