diff --git a/native/v8_extensions/native.mm b/native/v8_extensions/native.mm
index 71a975c8f..b34b68145 100644
--- a/native/v8_extensions/native.mm
+++ b/native/v8_extensions/native.mm
@@ -166,8 +166,7 @@ namespace v8_extensions {
     }
     else if (name == "traverseTree") {
       std::string argument = arguments[0]->GetStringValue().ToString();
-      int rootPathLength = argument.size();
-      char rootPath[rootPathLength + 1];
+      char rootPath[argument.size() + 1];
       strcpy(rootPath, argument.c_str());
       char * const paths[] = {rootPath, NULL};
 
@@ -191,12 +190,8 @@ namespace v8_extensions {
           continue;
         }
 
-        int pathLength = entry->fts_pathlen - rootPathLength;
-        char relative[pathLength + 1];
-        relative[pathLength] = '\0';
-        strncpy(relative, entry->fts_path + rootPathLength, pathLength);
         args.clear();
-        args.push_back(CefV8Value::CreateString(relative));
+        args.push_back(CefV8Value::CreateString(entry->fts_path));
         if (isFile) {
           onFile->ExecuteFunction(onFile, args);
         }
diff --git a/spec/stdlib/fs-spec.coffee b/spec/stdlib/fs-spec.coffee
index b0a6fae5f..94445d011 100644
--- a/spec/stdlib/fs-spec.coffee
+++ b/spec/stdlib/fs-spec.coffee
@@ -86,7 +86,7 @@ describe "fs", ->
     it "calls fn for every path in the tree at the given path", ->
       paths = []
       onPath = (path) ->
-        paths.push(fs.join(fixturesDir, path))
+        paths.push(path)
         true
       fs.traverseTree fixturesDir, onPath, onPath
       expect(paths).toEqual fs.listTree(fixturesDir)
@@ -106,14 +106,16 @@ describe "fs", ->
         expect(path).not.toMatch /\/dir\//
 
     it "returns entries if path is a symlink", ->
+      symlinkPath = fs.join(fixturesDir, 'symlink-to-dir')
       symlinkPaths = []
-      onSymlinkPath = (path) -> symlinkPaths.push(path)
+      onSymlinkPath = (path) -> symlinkPaths.push(path.substring(symlinkPath.length + 1))
 
+      regularPath = fs.join(fixturesDir, 'dir')
       paths = []
-      onPath = (path) -> paths.push(path)
+      onPath = (path) -> paths.push(path.substring(regularPath.length + 1))
 
-      fs.traverseTree(fs.join(fixturesDir, 'symlink-to-dir'), onSymlinkPath, onSymlinkPath)
-      fs.traverseTree(fs.join(fixturesDir, 'dir'), onPath, onPath)
+      fs.traverseTree(symlinkPath, onSymlinkPath, onSymlinkPath)
+      fs.traverseTree(regularPath, onPath, onPath)
 
       expect(symlinkPaths).toEqual(paths)
 
diff --git a/src/app/config.coffee b/src/app/config.coffee
index 2940b33f4..7c22c362e 100644
--- a/src/app/config.coffee
+++ b/src/app/config.coffee
@@ -37,16 +37,16 @@ class Config
     templateConfigDirPath = fs.resolve(window.resourcePath, 'dot-atom')
 
     onConfigDirFile = (path) =>
-      templatePath = fs.join(templateConfigDirPath, path)
-      configPath = fs.join(@configDirPath, path)
-      fs.write(configPath, fs.read(templatePath))
+      relativePath = path.substring(templateConfigDirPath.length + 1)
+      configPath = fs.join(@configDirPath, relativePath)
+      fs.write(configPath, fs.read(path))
     fs.traverseTree(templateConfigDirPath, onConfigDirFile, (path) -> true)
 
     configThemeDirPath = fs.join(@configDirPath, 'themes')
     onThemeDirFile = (path) ->
-      templatePath = fs.join(bundledThemesDirPath, path)
-      configPath = fs.join(configThemeDirPath, path)
-      fs.write(configPath, fs.read(templatePath))
+      relativePath = path.substring(bundledThemesDirPath.length + 1)
+      configPath = fs.join(configThemeDirPath, relativePath)
+      fs.write(configPath, fs.read(path))
     fs.traverseTree(bundledThemesDirPath, onThemeDirFile, (path) -> true)
 
   load: ->
diff --git a/src/packages/fuzzy-finder/lib/load-paths-handler.coffee b/src/packages/fuzzy-finder/lib/load-paths-handler.coffee
index 9ef442c99..ac7c338dc 100644
--- a/src/packages/fuzzy-finder/lib/load-paths-handler.coffee
+++ b/src/packages/fuzzy-finder/lib/load-paths-handler.coffee
@@ -13,8 +13,10 @@ module.exports =
         return true if _.contains(ignoredNames, segment)
       repo?.isPathIgnored(fs.join(rootPath, path))
     onFile = (path) ->
+      path = path.substring(rootPath.length + 1)
       paths.push(path) unless isIgnored(path)
     onDirectory = (path) ->
+      path = path.substring(rootPath.length + 1)
       not isIgnored(path)
     fs.traverseTree(rootPath, onFile, onDirectory)
 
diff --git a/src/stdlib/fs.coffee b/src/stdlib/fs.coffee
index cac22e5fe..5d9ffe226 100644
--- a/src/stdlib/fs.coffee
+++ b/src/stdlib/fs.coffee
@@ -63,11 +63,11 @@ module.exports =
     paths = []
     if extensions
       onPath = (path) =>
-        paths.push(@join(rootPath, path)) if _.contains(extensions, @extension(path))
+        paths.push(path) if _.contains(extensions, @extension(path))
         false
     else
       onPath = (path) =>
-        paths.push(@join(rootPath, path))
+        paths.push(path)
         false
     @traverseTree(rootPath, onPath, onPath)
     paths
@@ -75,7 +75,7 @@ module.exports =
   listTree: (rootPath) ->
     paths = []
     onPath = (path) =>
-      paths.push(@join(rootPath, path))
+      paths.push(path)
       true
     @traverseTree(rootPath, onPath, onPath)
     paths