From dbd8ef7fdbe0e20a77f0a86a1b9ad69eabb7f101 Mon Sep 17 00:00:00 2001
From: Brendan Kellam <bshizzle1234@gmail.com>
Date: Thu, 24 Jul 2025 10:21:00 -0700
Subject: [PATCH] fix: Fix issue with ambiguous references (#393)

---
 packages/web/src/features/chat/agent.ts       |  22 +--
 .../chatThread/codeFoldingExtension.test.ts   | 140 +++++++++++-------
 .../chatThread/markdownRenderer.tsx           |   5 +-
 .../chatThread/referencedSourcesListView.tsx  |   5 +-
 packages/web/src/features/chat/constants.ts   |   6 +-
 packages/web/src/features/chat/types.ts       |   3 +-
 .../chat/useExtractReferences.test.ts         |  54 ++++---
 .../src/features/chat/useExtractReferences.ts |   5 +-
 packages/web/src/features/chat/utils.test.ts  |  64 ++++----
 packages/web/src/features/chat/utils.ts       |  23 +--
 10 files changed, 191 insertions(+), 136 deletions(-)

diff --git a/packages/web/src/features/chat/agent.ts b/packages/web/src/features/chat/agent.ts
index 96d6540c..7f3ef93d 100644
--- a/packages/web/src/features/chat/agent.ts
+++ b/packages/web/src/features/chat/agent.ts
@@ -200,19 +200,19 @@ When you have sufficient context, output your answer as a structured markdown re
 **Required Response Format:**
 - **CRITICAL**: You MUST always prefix your answer with a \`${ANSWER_TAG}\` tag at the very top of your response
 - **CRITICAL**: You MUST provide your complete response in markdown format with embedded code references
-- **CODE REFERENCE REQUIREMENT**: Whenever you mention, discuss, or refer to ANY specific part of the code (files, functions, variables, methods, classes, imports, etc.), you MUST immediately follow with a code reference using the format \`${fileReferenceToString({ fileName: 'filename'})}\` or \`${fileReferenceToString({ fileName: 'filename', range: { startLine: 1, endLine: 10 } })}\` (where the numbers are the start and end line numbers of the code snippet). This includes:
-  - Files (e.g., "The \`auth.ts\` file" → must include \`${fileReferenceToString({ fileName: 'auth.ts' })}\`)
-  - Function names (e.g., "The \`getRepos()\` function" → must include \`${fileReferenceToString({ fileName: 'auth.ts', range: { startLine: 15, endLine: 20 } })}\`)
-  - Variable names (e.g., "The \`suggestionQuery\` variable" → must include \`${fileReferenceToString({ fileName: 'search.ts', range: { startLine: 42, endLine: 42 } })}\`)
-  - Code patterns (e.g., "using \`file:\${suggestionQuery}\` pattern" → must include \`${fileReferenceToString({ fileName: 'search.ts', range: { startLine: 10, endLine: 15 } })}\`)
+- **CODE REFERENCE REQUIREMENT**: Whenever you mention, discuss, or refer to ANY specific part of the code (files, functions, variables, methods, classes, imports, etc.), you MUST immediately follow with a code reference using the format \`${fileReferenceToString({ repo: 'repository', path: 'filename'})}\` or \`${fileReferenceToString({ repo: 'repository', path: 'filename', range: { startLine: 1, endLine: 10 } })}\` (where the numbers are the start and end line numbers of the code snippet). This includes:
+  - Files (e.g., "The \`auth.ts\` file" → must include \`${fileReferenceToString({ repo: 'repository', path: 'auth.ts' })}\`)
+  - Function names (e.g., "The \`getRepos()\` function" → must include \`${fileReferenceToString({ repo: 'repository', path: 'auth.ts', range: { startLine: 15, endLine: 20 } })}\`)
+  - Variable names (e.g., "The \`suggestionQuery\` variable" → must include \`${fileReferenceToString({ repo: 'repository', path: 'search.ts', range: { startLine: 42, endLine: 42 } })}\`)
   - Any code snippet or line you're explaining
   - Class names, method calls, imports, etc.
 - Some examples of both correct and incorrect code references:
-  - Correct: @file:{path/to/file.ts}
-  - Correct: @file:{path/to/file.ts:10-15}
-  - Incorrect: @file{path/to/file.ts} (missing colon)
-  - Incorrect: @file:path/to/file.ts (missing curly braces)
-  - Incorrect: @file:{path/to/file.ts:10-25,30-35} (multiple ranges not supported)
+  - Correct: @file:{repository::path/to/file.ts}
+  - Correct: @file:{repository::path/to/file.ts:10-15}
+  - Incorrect: @file{repository::path/to/file.ts} (missing colon)
+  - Incorrect: @file:repository::path/to/file.ts (missing curly braces)
+  - Incorrect: @file:{repository::path/to/file.ts:10-25,30-35} (multiple ranges not supported)
+  - Incorrect: @file:{path/to/file.ts} (missing repository)
 - Be clear and very concise. Use bullet points where appropriate
 - Do NOT explain code without providing the exact location reference. Every code mention requires a corresponding \`${FILE_REFERENCE_PREFIX}\` reference
 - If you cannot provide a code reference for something you're discussing, do not mention that specific code element
@@ -221,7 +221,7 @@ When you have sufficient context, output your answer as a structured markdown re
 **Example answer structure:**
 \`\`\`markdown
 ${ANSWER_TAG}
-Authentication in Sourcebot is built on NextAuth.js with a session-based approach using JWT tokens and Prisma as the database adapter ${fileReferenceToString({ fileName: 'auth.ts', range: { startLine: 135, endLine: 140 } })}. The system supports multiple authentication providers and implements organization-based authorization with role-defined permissions.
+Authentication in Sourcebot is built on NextAuth.js with a session-based approach using JWT tokens and Prisma as the database adapter ${fileReferenceToString({ repo: 'github.com/sourcebot-dev/sourcebot', path: 'auth.ts', range: { startLine: 135, endLine: 140 } })}. The system supports multiple authentication providers and implements organization-based authorization with role-defined permissions.
 \`\`\`
 
 </answer_instructions>
diff --git a/packages/web/src/features/chat/components/chatThread/codeFoldingExtension.test.ts b/packages/web/src/features/chat/components/chatThread/codeFoldingExtension.test.ts
index b0b1e9a8..920cc129 100644
--- a/packages/web/src/features/chat/components/chatThread/codeFoldingExtension.test.ts
+++ b/packages/web/src/features/chat/components/chatThread/codeFoldingExtension.test.ts
@@ -17,13 +17,14 @@ describe('calculateVisibleRanges', () => {
     test('applies padding to a single range', () => {
         const references: FileReference[] = [
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '1',
                 type: 'file',
                 range: {
                     startLine: 10,
                     endLine: 15
-                }
+                },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             }
         ];
 
@@ -38,16 +39,18 @@ describe('calculateVisibleRanges', () => {
     test('merges overlapping ranges', () => {
         const references: FileReference[] = [
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '1',
                 type: 'file',
-                range: { startLine: 10, endLine: 15 }
+                range: { startLine: 10, endLine: 15 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             },
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '2',
                 type: 'file',
-                range: { startLine: 12, endLine: 20 }
+                range: { startLine: 12, endLine: 20 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             }
         ];
 
@@ -62,16 +65,18 @@ describe('calculateVisibleRanges', () => {
     test('merges adjacent ranges (including padding)', () => {
         const references: FileReference[] = [
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '1',
                 type: 'file',
-                range: { startLine: 10, endLine: 15 }
+                range: { startLine: 10, endLine: 15 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             },
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '2',
                 type: 'file',
-                range: { startLine: 19, endLine: 25 }
+                range: { startLine: 19, endLine: 25 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             }
         ];
 
@@ -88,16 +93,18 @@ describe('calculateVisibleRanges', () => {
     test('keeps separate ranges when they dont overlap', () => {
         const references: FileReference[] = [
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '1',
                 type: 'file',
-                range: { startLine: 10, endLine: 15 }
+                range: { startLine: 10, endLine: 15 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             },
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '2',
                 type: 'file',
-                range: { startLine: 25, endLine: 30 }
+                range: { startLine: 25, endLine: 30 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             }
         ];
 
@@ -112,10 +119,11 @@ describe('calculateVisibleRanges', () => {
     test('respects file boundaries - start of file', () => {
         const references: FileReference[] = [
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '1',
                 type: 'file',
-                range: { startLine: 1, endLine: 5 }
+                range: { startLine: 1, endLine: 5 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             }
         ];
 
@@ -130,10 +138,11 @@ describe('calculateVisibleRanges', () => {
     test('respects file boundaries - end of file', () => {
         const references: FileReference[] = [
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '1',
                 type: 'file',
-                range: { startLine: 95, endLine: 100 }
+                range: { startLine: 95, endLine: 100 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             }
         ];
 
@@ -148,28 +157,32 @@ describe('calculateVisibleRanges', () => {
     test('handles multiple ranges with complex overlaps', () => {
         const references: FileReference[] = [
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '1',
                 type: 'file',
-                range: { startLine: 10, endLine: 15 }
+                range: { startLine: 10, endLine: 15 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             },
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '2',
                 type: 'file',
-                range: { startLine: 20, endLine: 25 }
+                range: { startLine: 20, endLine: 25 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             },
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '3',
                 type: 'file',
-                range: { startLine: 22, endLine: 30 }
+                range: { startLine: 22, endLine: 30 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             },
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '4',
                 type: 'file',
-                range: { startLine: 50, endLine: 55 }
+                range: { startLine: 50, endLine: 55 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             }
         ];
 
@@ -195,16 +208,18 @@ describe('calculateVisibleRanges', () => {
     test('ignores references without ranges', () => {
         const references: FileReference[] = [
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '1',
                 type: 'file',
                 // No range property
+                repo: 'github.com/sourcebot-dev/sourcebot'
             },
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '2',
                 type: 'file',
-                range: { startLine: 10, endLine: 15 }
+                range: { startLine: 10, endLine: 15 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             }
         ];
 
@@ -219,10 +234,11 @@ describe('calculateVisibleRanges', () => {
     test('works with zero padding', () => {
         const references: FileReference[] = [
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '1',
                 type: 'file',
-                range: { startLine: 10, endLine: 15 }
+                range: { startLine: 10, endLine: 15 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             }
         ];
 
@@ -237,10 +253,11 @@ describe('calculateVisibleRanges', () => {
     test('handles single line ranges', () => {
         const references: FileReference[] = [
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '1',
                 type: 'file',
-                range: { startLine: 10, endLine: 10 }
+                range: { startLine: 10, endLine: 10 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             }
         ];
 
@@ -255,22 +272,25 @@ describe('calculateVisibleRanges', () => {
     test('sorts ranges by start line', () => {
         const references: FileReference[] = [
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '1',
                 type: 'file',
-                range: { startLine: 50, endLine: 55 }
+                range: { startLine: 50, endLine: 55 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             },
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '2',
                 type: 'file',
-                range: { startLine: 10, endLine: 15 }
+                range: { startLine: 10, endLine: 15 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             },
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '3',
                 type: 'file',
-                range: { startLine: 30, endLine: 35 }
+                range: { startLine: 30, endLine: 35 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             }
         ];
 
@@ -380,16 +400,18 @@ describe('StateField Integration', () => {
     test('initial state calculation with references', () => {
         const references: FileReference[] = [
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '1',
                 type: 'file',
-                range: { startLine: 10, endLine: 15 }
+                range: { startLine: 10, endLine: 15 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             },
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '2',
                 type: 'file',
-                range: { startLine: 25, endLine: 30 }
+                range: { startLine: 25, endLine: 30 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             }
         ];
 
@@ -457,7 +479,7 @@ describe('StateField Integration', () => {
         // Update references
         const newReferences: FileReference[] = [
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '1',
                 type: 'file',
                 range: { startLine: 10, endLine: 15 }
@@ -482,10 +504,11 @@ describe('StateField Integration', () => {
     test('expandRegionEffect expands hidden region up', () => {
         const references: FileReference[] = [
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '1',
                 type: 'file',
-                range: { startLine: 20, endLine: 25 }
+                range: { startLine: 20, endLine: 25 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             }
         ];
 
@@ -528,10 +551,11 @@ describe('StateField Integration', () => {
     test('expandRegionEffect expands hidden region down', () => {
         const references: FileReference[] = [
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '1',
                 type: 'file',
-                range: { startLine: 20, endLine: 25 }
+                range: { startLine: 20, endLine: 25 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             }
         ];
 
@@ -564,10 +588,11 @@ describe('StateField Integration', () => {
     test('document changes recalculate state', () => {
         const references: FileReference[] = [
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '1',
                 type: 'file',
-                range: { startLine: 10, endLine: 15 }
+                range: { startLine: 10, endLine: 15 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             }
         ];
 
@@ -606,10 +631,11 @@ describe('StateField Integration', () => {
     test('action creators work correctly', () => {
         const references: FileReference[] = [
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '1',
                 type: 'file',
-                range: { startLine: 10, endLine: 15 }
+                range: { startLine: 10, endLine: 15 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             }
         ];
 
@@ -647,16 +673,18 @@ describe('StateField Integration', () => {
         // Add references
         const references: FileReference[] = [
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '1',
                 type: 'file',
-                range: { startLine: 20, endLine: 25 }
+                range: { startLine: 20, endLine: 25 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             },
             {
-                fileName: 'test.ts',
+                path: 'test.ts',
                 id: '2',
                 type: 'file',
-                range: { startLine: 60, endLine: 65 }
+                range: { startLine: 60, endLine: 65 },
+                repo: 'github.com/sourcebot-dev/sourcebot'
             }
         ];
 
diff --git a/packages/web/src/features/chat/components/chatThread/markdownRenderer.tsx b/packages/web/src/features/chat/components/chatThread/markdownRenderer.tsx
index 3daeeeba..17a27937 100644
--- a/packages/web/src/features/chat/components/chatThread/markdownRenderer.tsx
+++ b/packages/web/src/features/chat/components/chatThread/markdownRenderer.tsx
@@ -45,12 +45,13 @@ function remarkReferencesPlugin() {
     return function (tree: Nodes) {
         findAndReplace(tree, [
             FILE_REFERENCE_REGEX,
-            (_, fileName: string, startLine?: string, endLine?: string) => {
+            (_, repo: string, fileName: string, startLine?: string, endLine?: string) => {
                 // Create display text
                 let displayText = fileName.split('/').pop() ?? fileName;
 
                 const fileReference = createFileReference({
-                    fileName,
+                    repo: repo,
+                    path: fileName,
                     startLine,
                     endLine,
                 });
diff --git a/packages/web/src/features/chat/components/chatThread/referencedSourcesListView.tsx b/packages/web/src/features/chat/components/chatThread/referencedSourcesListView.tsx
index c930cee9..c7a0c087 100644
--- a/packages/web/src/features/chat/components/chatThread/referencedSourcesListView.tsx
+++ b/packages/web/src/features/chat/components/chatThread/referencedSourcesListView.tsx
@@ -36,7 +36,10 @@ interface ReferencedSourcesListViewProps {
 }
 
 const resolveFileReference = (reference: FileReference, sources: FileSource[]): FileSource | undefined => {
-    return sources.find((source) => source.path.endsWith(reference.fileName));
+    return sources.find(
+        (source) => source.repo.endsWith(reference.repo) &&
+        source.path.endsWith(reference.path)
+    );
 }
 
 const getFileId = (fileSource: FileSource) => {
diff --git a/packages/web/src/features/chat/constants.ts b/packages/web/src/features/chat/constants.ts
index 06ae94c9..6ba38f09 100644
--- a/packages/web/src/features/chat/constants.ts
+++ b/packages/web/src/features/chat/constants.ts
@@ -1,6 +1,10 @@
 
 export const FILE_REFERENCE_PREFIX = '@file:';
-export const FILE_REFERENCE_REGEX = new RegExp(`${FILE_REFERENCE_PREFIX}\\{([^:}]+)(?::(\\d+)(?:-(\\d+))?)?\\}`, 'g');
+export const FILE_REFERENCE_REGEX = new RegExp(
+    // @file:{repoName::fileName:startLine-endLine}
+    `${FILE_REFERENCE_PREFIX}\\{([^:}]+)::([^:}]+)(?::(\\d+)(?:-(\\d+))?)?\\}`, 
+    'g'
+);
 
 export const ANSWER_TAG = '<!--answer-->';
 
diff --git a/packages/web/src/features/chat/types.ts b/packages/web/src/features/chat/types.ts
index cd1f078b..8b04c88e 100644
--- a/packages/web/src/features/chat/types.ts
+++ b/packages/web/src/features/chat/types.ts
@@ -25,7 +25,8 @@ export type Source = z.infer<typeof sourceSchema>;
 const fileReferenceSchema = z.object({
     type: z.literal('file'),
     id: z.string(),
-    fileName: z.string(),
+    repo: z.string(),
+    path: z.string(),
     range: z.object({
         startLine: z.number(),
         endLine: z.number(),
diff --git a/packages/web/src/features/chat/useExtractReferences.test.ts b/packages/web/src/features/chat/useExtractReferences.test.ts
index 940129f4..b2121e6c 100644
--- a/packages/web/src/features/chat/useExtractReferences.test.ts
+++ b/packages/web/src/features/chat/useExtractReferences.test.ts
@@ -11,7 +11,7 @@ test('useExtractReferences extracts file references from text content', () => {
         parts: [
                 {
                     type: 'text',
-                    text: 'The auth flow is implemented in @file:{auth.ts} and uses sessions @file:{auth.ts:45-60}.'
+                    text: 'The auth flow is implemented in @file:{github.com/sourcebot-dev/sourcebot::auth.ts} and uses sessions @file:{github.com/sourcebot-dev/sourcebot::auth.ts:45-60}.'
                 }
         ]
     };
@@ -20,15 +20,18 @@ test('useExtractReferences extracts file references from text content', () => {
 
     expect(result.current).toHaveLength(2);
     expect(result.current[0]).toMatchObject({
-        fileName: 'auth.ts',
-        id: getFileReferenceId({ fileName: 'auth.ts' }),
+        repo: 'github.com/sourcebot-dev/sourcebot',
+        path: 'auth.ts',
+        id: getFileReferenceId({ repo: 'github.com/sourcebot-dev/sourcebot', path: 'auth.ts' }),
         type: 'file',
     });
 
     expect(result.current[1]).toMatchObject({
-        fileName: 'auth.ts',
+        repo: 'github.com/sourcebot-dev/sourcebot',
+        path: 'auth.ts',
         id: getFileReferenceId({
-            fileName: 'auth.ts',
+            repo: 'github.com/sourcebot-dev/sourcebot',
+            path: 'auth.ts',
             range: {
                 startLine: 45,
                 endLine: 60,
@@ -49,7 +52,7 @@ test('useExtractReferences extracts file references from reasoning content', ()
         parts: [
                 {
                     type: 'reasoning',
-                    text: 'The auth flow is implemented in @file:{auth.ts} and uses sessions @file:{auth.ts:45-60}.'
+                    text: 'The auth flow is implemented in @file:{github.com/sourcebot-dev/sourcebot::auth.ts} and uses sessions @file:{github.com/sourcebot-dev/sourcebot::auth.ts:45-60}.'
                 }
         ]
     };
@@ -58,15 +61,18 @@ test('useExtractReferences extracts file references from reasoning content', ()
 
     expect(result.current).toHaveLength(2);
     expect(result.current[0]).toMatchObject({
-        fileName: 'auth.ts',
-        id: getFileReferenceId({ fileName: 'auth.ts' }),
+        repo: 'github.com/sourcebot-dev/sourcebot',
+        path: 'auth.ts',
+        id: getFileReferenceId({ repo: 'github.com/sourcebot-dev/sourcebot', path: 'auth.ts' }),
         type: 'file',
     });
 
     expect(result.current[1]).toMatchObject({
-        fileName: 'auth.ts',
+        repo: 'github.com/sourcebot-dev/sourcebot',
+        path: 'auth.ts',
         id: getFileReferenceId({
-            fileName: 'auth.ts',
+            repo: 'github.com/sourcebot-dev/sourcebot',
+            path: 'auth.ts',
             range: {
                 startLine: 45,
                 endLine: 60,
@@ -87,15 +93,15 @@ test('useExtractReferences extracts file references from multi-part', () => {
         parts: [
             {
                 type: 'text',
-                text: 'The auth flow is implemented in @file:{auth.ts}.'
+                text: 'The auth flow is implemented in @file:{github.com/sourcebot-dev/sourcebot::auth.ts}.'
             },
             {
                 type: 'reasoning',
-                text: 'We need to check the session handling in @file:{session.ts:10-20}.'
+                text: 'We need to check the session handling in @file:{github.com/sourcebot-dev/sourcebot::session.ts:10-20}.'
             },
             {
                 type: 'text',
-                text: 'The configuration is stored in @file:{config.json} and @file:{utils.ts:5}.'
+                text: 'The configuration is stored in @file:{github.com/sourcebot-dev/sourcebot::config.json} and @file:{github.com/sourcebot-dev/sourcebot::utils.ts:5}.'
             }
         ]
     };
@@ -106,16 +112,19 @@ test('useExtractReferences extracts file references from multi-part', () => {
     
     // From text part
     expect(result.current[0]).toMatchObject({
-        fileName: 'auth.ts',
-        id: getFileReferenceId({ fileName: 'auth.ts' }),
+        repo: 'github.com/sourcebot-dev/sourcebot',
+        path: 'auth.ts',
+        id: getFileReferenceId({ repo: 'github.com/sourcebot-dev/sourcebot', path: 'auth.ts' }),
         type: 'file',
     });
 
     // From reasoning part
     expect(result.current[1]).toMatchObject({
-        fileName: 'session.ts',
+        repo: 'github.com/sourcebot-dev/sourcebot',
+        path: 'session.ts',
         id: getFileReferenceId({
-            fileName: 'session.ts',
+            repo: 'github.com/sourcebot-dev/sourcebot',
+            path: 'session.ts',
             range: {
                 startLine: 10,
                 endLine: 20,
@@ -129,15 +138,18 @@ test('useExtractReferences extracts file references from multi-part', () => {
     });
 
     expect(result.current[2]).toMatchObject({
-        fileName: 'config.json',
-        id: getFileReferenceId({ fileName: 'config.json' }),
+        repo: 'github.com/sourcebot-dev/sourcebot',
+        path: 'config.json',
+        id: getFileReferenceId({ repo: 'github.com/sourcebot-dev/sourcebot', path: 'config.json' }),
         type: 'file',
     });
 
     expect(result.current[3]).toMatchObject({
-        fileName: 'utils.ts',
+        repo: 'github.com/sourcebot-dev/sourcebot',
+        path: 'utils.ts',
         id: getFileReferenceId({
-            fileName: 'utils.ts',
+            repo: 'github.com/sourcebot-dev/sourcebot',
+            path: 'utils.ts',
             range: {
                 startLine: 5,
                 endLine: 5,
diff --git a/packages/web/src/features/chat/useExtractReferences.ts b/packages/web/src/features/chat/useExtractReferences.ts
index 4ab558c7..b3eecf97 100644
--- a/packages/web/src/features/chat/useExtractReferences.ts
+++ b/packages/web/src/features/chat/useExtractReferences.ts
@@ -18,10 +18,11 @@ export const useExtractReferences = (message?: SBChatMessage) => {
 
                     let match;
                     while ((match = FILE_REFERENCE_REGEX.exec(content ?? '')) !== null && match !== null) {
-                        const [_, fileName, startLine, endLine] = match;
+                        const [_, repo, fileName, startLine, endLine] = match;
 
                         const fileReference = createFileReference({
-                            fileName,
+                            repo: repo,
+                            path: fileName,
                             startLine,
                             endLine,
                         });
diff --git a/packages/web/src/features/chat/utils.test.ts b/packages/web/src/features/chat/utils.test.ts
index 00d5c55b..af78fa6d 100644
--- a/packages/web/src/features/chat/utils.test.ts
+++ b/packages/web/src/features/chat/utils.test.ts
@@ -13,26 +13,30 @@ vi.mock('@/env.mjs', () => ({
 
 test('fileReferenceToString formats file references correctly', () => {
     expect(fileReferenceToString({
-        fileName: 'auth.ts'
-    })).toBe('@file:{auth.ts}');
+        repo: 'github.com/sourcebot-dev/sourcebot',
+        path: 'auth.ts'
+    })).toBe('@file:{github.com/sourcebot-dev/sourcebot::auth.ts}');
 
     expect(fileReferenceToString({
-        fileName: 'auth.ts',
+        repo: 'github.com/sourcebot-dev/sourcebot',
+        path: 'auth.ts',
         range: {
             startLine: 45,
             endLine: 60,
         }
-    })).toBe('@file:{auth.ts:45-60}');
+    })).toBe('@file:{github.com/sourcebot-dev/sourcebot::auth.ts:45-60}');
 });
 
 test('fileReferenceToString matches FILE_REFERENCE_REGEX', () => {
     expect(FILE_REFERENCE_REGEX.test(fileReferenceToString({
-        fileName: 'auth.ts'
+        repo: 'github.com/sourcebot-dev/sourcebot',
+        path: 'auth.ts'
     }))).toBe(true);
 
     FILE_REFERENCE_REGEX.lastIndex = 0;
     expect(FILE_REFERENCE_REGEX.test(fileReferenceToString({
-        fileName: 'auth.ts',
+        repo: 'github.com/sourcebot-dev/sourcebot',
+        path: 'auth.ts',
         range: {
             startLine: 45,
             endLine: 60,
@@ -240,55 +244,55 @@ test('getAnswerPartFromAssistantMessage returns undefined when streaming and no
 });
 
 test('repairCitations fixes missing colon after @file', () => {
-    const input = 'See the function in @file{auth.ts} for details.';
-    const expected = 'See the function in @file:{auth.ts} for details.';
+    const input = 'See the function in @file{github.com/sourcebot-dev/sourcebot::auth.ts} for details.';
+    const expected = 'See the function in @file:{github.com/sourcebot-dev/sourcebot::auth.ts} for details.';
     expect(repairCitations(input)).toBe(expected);
 });
 
 test('repairCitations fixes missing colon with range', () => {
-    const input = 'Check @file{config.ts:15-20} for the configuration.';
-    const expected = 'Check @file:{config.ts:15-20} for the configuration.';
+    const input = 'Check @file{github.com/sourcebot-dev/sourcebot::config.ts:15-20} for the configuration.';
+    const expected = 'Check @file:{github.com/sourcebot-dev/sourcebot::config.ts:15-20} for the configuration.';
     expect(repairCitations(input)).toBe(expected);
 });
 
 test('repairCitations fixes missing braces around filename', () => {
-    const input = 'The logic is in @file:utils.js and handles validation.';
-    const expected = 'The logic is in @file:{utils.js} and handles validation.';
+    const input = 'The logic is in @file:github.com/sourcebot-dev/sourcebot::utils.js and handles validation.';
+    const expected = 'The logic is in @file:{github.com/sourcebot-dev/sourcebot::utils.js} and handles validation.';
     expect(repairCitations(input)).toBe(expected);
 });
 
 test('repairCitations fixes missing braces with path', () => {
-    const input = 'Look at @file:src/components/Button.tsx for the component.';
-    const expected = 'Look at @file:{src/components/Button.tsx} for the component.';
+    const input = 'Look at @file:github.com/sourcebot-dev/sourcebot::src/components/Button.tsx for the component.';
+    const expected = 'Look at @file:{github.com/sourcebot-dev/sourcebot::src/components/Button.tsx} for the component.';
     expect(repairCitations(input)).toBe(expected);
 });
 
 test('repairCitations removes multiple ranges keeping only first', () => {
-    const input = 'See @file:{service.ts:10-15,20-25,30-35} for implementation.';
-    const expected = 'See @file:{service.ts:10-15} for implementation.';
+    const input = 'See @file:{github.com/sourcebot-dev/sourcebot::service.ts:10-15,20-25,30-35} for implementation.';
+    const expected = 'See @file:{github.com/sourcebot-dev/sourcebot::service.ts:10-15} for implementation.';
     expect(repairCitations(input)).toBe(expected);
 });
 
 test('repairCitations fixes malformed triple number ranges', () => {
-    const input = 'Check @file:{handler.ts:5-10-15} for the logic.';
-    const expected = 'Check @file:{handler.ts:5-10} for the logic.';
+    const input = 'Check @file:{github.com/sourcebot-dev/sourcebot::handler.ts:5-10-15} for the logic.';
+    const expected = 'Check @file:{github.com/sourcebot-dev/sourcebot::handler.ts:5-10} for the logic.';
     expect(repairCitations(input)).toBe(expected);
 });
 
 test('repairCitations handles multiple citations in same text', () => {
-    const input = 'See @file{auth.ts} and @file:config.js for setup details.';
-    const expected = 'See @file:{auth.ts} and @file:{config.js} for setup details.';
+    const input = 'See @file{github.com/sourcebot-dev/sourcebot::auth.ts} and @file:github.com/sourcebot-dev/sourcebot::config.js for setup details.';
+    const expected = 'See @file:{github.com/sourcebot-dev/sourcebot::auth.ts} and @file:{github.com/sourcebot-dev/sourcebot::config.js} for setup details.';
     expect(repairCitations(input)).toBe(expected);
 });
 
 test('repairCitations leaves correctly formatted citations unchanged', () => {
-    const input = 'The function @file:{utils.ts:42-50} handles validation correctly.';
+    const input = 'The function @file:{github.com/sourcebot-dev/sourcebot::utils.ts:42-50} handles validation correctly.';
     expect(repairCitations(input)).toBe(input);
 });
 
 test('repairCitations handles edge cases with spaces and punctuation', () => {
-    const input = 'Functions like @file:helper.ts, @file{main.js}, and @file:{app.ts:1-5,10-15} work.';
-    const expected = 'Functions like @file:{helper.ts}, @file:{main.js}, and @file:{app.ts:1-5} work.';
+    const input = 'Functions like @file:github.com/sourcebot-dev/sourcebot::helper.ts, @file{github.com/sourcebot-dev/sourcebot::main.js}, and @file:{github.com/sourcebot-dev/sourcebot::app.ts:1-5,10-15} work.';
+    const expected = 'Functions like @file:{github.com/sourcebot-dev/sourcebot::helper.ts}, @file:{github.com/sourcebot-dev/sourcebot::main.js}, and @file:{github.com/sourcebot-dev/sourcebot::app.ts:1-5} work.';
     expect(repairCitations(input)).toBe(expected);
 });
 
@@ -302,24 +306,24 @@ test('repairCitations returns text without citations unchanged', () => {
 });
 
 test('repairCitations handles complex file paths correctly', () => {
-    const input = 'Check @file:src/components/ui/Button/index.tsx for implementation.';
-    const expected = 'Check @file:{src/components/ui/Button/index.tsx} for implementation.';
+    const input = 'Check @file:github.com/sourcebot-dev/sourcebot::src/components/ui/Button/index.tsx for implementation.';
+    const expected = 'Check @file:{github.com/sourcebot-dev/sourcebot::src/components/ui/Button/index.tsx} for implementation.';
     expect(repairCitations(input)).toBe(expected);
 });
 
 test('repairCitations handles files with numbers and special characters', () => {
-    const input = 'See @file{utils-v2.0.1.ts} and @file:config_2024.json for setup.';
-    const expected = 'See @file:{utils-v2.0.1.ts} and @file:{config_2024.json} for setup.';
+    const input = 'See @file{github.com/sourcebot-dev/sourcebot::utils-v2.0.1.ts} and @file:github.com/sourcebot-dev/sourcebot::config_2024.json for setup.';
+    const expected = 'See @file:{github.com/sourcebot-dev/sourcebot::utils-v2.0.1.ts} and @file:{github.com/sourcebot-dev/sourcebot::config_2024.json} for setup.';
     expect(repairCitations(input)).toBe(expected);
 });
 
 test('repairCitations handles citation at end of sentence', () => {
-    const input = 'The implementation is in @file:helper.ts.';
-    const expected = 'The implementation is in @file:{helper.ts}.';
+    const input = 'The implementation is in @file:github.com/sourcebot-dev/sourcebot::helper.ts.';
+    const expected = 'The implementation is in @file:{github.com/sourcebot-dev/sourcebot::helper.ts}.';
     expect(repairCitations(input)).toBe(expected);
 });
 
 test('repairCitations preserves already correct citations with ranges', () => {
-    const input = 'The function @file:{utils.ts:10-20} and variable @file:{config.js:5} work correctly.';
+    const input = 'The function @file:{github.com/sourcebot-dev/sourcebot::utils.ts:10-20} and variable @file:{github.com/sourcebot-dev/sourcebot::config.js:5} work correctly.';
     expect(repairCitations(input)).toBe(input);
 });
diff --git a/packages/web/src/features/chat/utils.ts b/packages/web/src/features/chat/utils.ts
index 28c14228..ec1385b1 100644
--- a/packages/web/src/features/chat/utils.ts
+++ b/packages/web/src/features/chat/utils.ts
@@ -129,7 +129,7 @@ export const slateContentToString = (children: Descendant[]): string => {
 
             switch (type) {
                 case 'file':
-                    return `${fileReferenceToString({ fileName: child.data.name })} `;
+                    return `${fileReferenceToString({ repo: child.data.repo, path: child.data.path })} `;
             }
         }
 
@@ -210,15 +210,15 @@ export const createUIMessage = (text: string, mentions: MentionData[], selectedR
     }
 }
 
-export const getFileReferenceId = ({ fileName, range }: Omit<FileReference, 'type' | 'id'>) => {
-    return `file-reference-${fileName}${range ? `-${range.startLine}-${range.endLine}` : ''}`;
+export const getFileReferenceId = ({ repo, path, range }: Omit<FileReference, 'type' | 'id'>) => {
+    return `file-reference-${repo}::${path}${range ? `-${range.startLine}-${range.endLine}` : ''}`;
 }
 
-export const fileReferenceToString = ({ fileName, range }: Omit<FileReference, 'type' | 'id'>) => {
-    return `${FILE_REFERENCE_PREFIX}{${fileName}${range ? `:${range.startLine}-${range.endLine}` : ''}}`;
+export const fileReferenceToString = ({ repo, path, range }: Omit<FileReference, 'type' | 'id'>) => {
+    return `${FILE_REFERENCE_PREFIX}{${repo}::${path}${range ? `:${range.startLine}-${range.endLine}` : ''}}`;
 }
 
-export const createFileReference = ({ fileName, startLine, endLine }: { fileName: string, startLine?: string, endLine?: string }): FileReference => {
+export const createFileReference = ({ repo, path, startLine, endLine }: { repo: string, path: string, startLine?: string, endLine?: string }): FileReference => {
     const range = startLine && endLine ? {
         startLine: parseInt(startLine),
         endLine: parseInt(endLine),
@@ -229,8 +229,9 @@ export const createFileReference = ({ fileName, startLine, endLine }: { fileName
 
     return {
         type: 'file',
-        id: getFileReferenceId({ fileName, range }),
-        fileName,
+        id: getFileReferenceId({ repo, path, range }),
+        repo,
+        path,
         range,
     }
 }
@@ -241,7 +242,7 @@ export const createFileReference = ({ fileName, startLine, endLine }: { fileName
  * links.
  */
 export const convertLLMOutputToPortableMarkdown = (text: string): string => {
-    return text.replace(FILE_REFERENCE_REGEX, (_, fileName, startLine, endLine) => {
+    return text.replace(FILE_REFERENCE_REGEX, (_, _repo, fileName, startLine, endLine) => {
         const displayName = fileName.split('/').pop() || fileName;
 
         let linkText = displayName;
@@ -294,9 +295,9 @@ export const repairCitations = (text: string): string => {
         // Fix missing braces: @file:filename -> @file:{filename}
         .replace(/@file:([^\s{]\S*?)(\s|[,;!?](?:\s|$)|\.(?:\s|$)|$)/g, '@file:{$1}$2')
         // Fix multiple ranges: keep only first range
-        .replace(/@file:\{([^:}]+):(\d+-\d+),[\d,-]+\}/g, '@file:{$1:$2}')
+        .replace(/@file:\{(.+?):(\d+-\d+),[\d,-]+\}/g, '@file:{$1:$2}')
         // Fix malformed ranges
-        .replace(/@file:\{([^:}]+):(\d+)-(\d+)-(\d+)\}/g, '@file:{$1:$2-$3}');
+        .replace(/@file:\{(.+?):(\d+)-(\d+)-(\d+)\}/g, '@file:{$1:$2-$3}');
 };
 
 // Attempts to find the part of the assistant's message