@in-the-loop-labs/pair-review 2.1.0 → 2.1.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@in-the-loop-labs/pair-review",
-  "version": "2.1.0",
+  "version": "2.1.1",
   "description": "Your AI-powered code review partner - Close the feedback loop with AI coding agents",
   "main": "src/server.js",
   "bin": {

package/plugin/.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "pair-review",
-  "version": "2.1.0",
+  "version": "2.1.1",
   "description": "pair-review app integration — Open PRs and local changes in the pair-review web UI, run server-side AI analysis, and address review feedback. Requires the pair-review MCP server.",
   "author": {
     "name": "in-the-loop-labs",

package/plugin-code-critic/.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "code-critic",
-  "version": "2.1.0",
+  "version": "2.1.1",
   "description": "AI-powered code review analysis — Run three-level AI analysis and implement-review-fix loops directly in your coding agent. Works standalone, no server required.",
   "author": {
     "name": "in-the-loop-labs",

package/plugin-code-critic/skills/analyze/references/level1-balanced.md

@@ -92,6 +92,15 @@ Do NOT modify files or run write commands. Analyze and report only.
   "summary": "Brief summary of findings"
 }
 
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+```suggestion
+replacement content here
+```
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
+
 ## Line Number Reference (old_or_new field)
 The "old_or_new" field indicates which line number column to use:
 - **"NEW"** (default): Use the NEW column number for:

package/plugin-code-critic/skills/analyze/references/level1-fast.md

@@ -78,6 +78,15 @@ Annotated diff tool, `cat -n`, ls, find, grep. Do NOT modify files.
   "summary": "Brief summary"
 }
 
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+```suggestion
+replacement content here
+```
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
+
 ## Line Numbers (old_or_new)
 - "NEW" (default): added [+] and context lines
 - "OLD": deleted [-] lines only

package/plugin-code-critic/skills/analyze/references/level1-thorough.md

@@ -138,6 +138,15 @@ Output JSON with this structure:
   "summary": "Brief summary of findings"
 }
 
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+```suggestion
+replacement content here
+```
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
+
 ## Line Number Reference (old_or_new field)
 The "old_or_new" field indicates which line number column to use:
 - **"NEW"** (default): Use the NEW column number. This is correct for:

package/plugin-code-critic/skills/analyze/references/level2-balanced.md

@@ -103,6 +103,15 @@ Note: You may use parallel read-only Tasks to examine multiple files simultaneou
   "summary": "Brief summary of file context findings"
 }
 
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+```suggestion
+replacement content here
+```
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
+
 ## Line Number Reference (old_or_new field)
 - **"NEW"** (default): For ADDED [+] lines and CONTEXT lines
 - **"OLD"**: ONLY for DELETED [-] lines

package/plugin-code-critic/skills/analyze/references/level2-fast.md

@@ -87,6 +87,15 @@ Annotated diff tool (preferred), `cat -n <file>`, ls, find, grep. Do NOT modify
   "summary": "Brief summary"
 }
 
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+```suggestion
+replacement content here
+```
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
+
 ## Line Numbers
 "NEW" (default): added [+] and context lines. "OLD": only deleted [-] lines.
 

package/plugin-code-critic/skills/analyze/references/level2-thorough.md

@@ -177,6 +177,15 @@ Output JSON with this structure:
   "summary": "Brief summary of file context findings"
 }
 
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+```suggestion
+replacement content here
+```
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
+
 ## old_or_new Field Reference
 Use "NEW" (the default) for added lines [+] and context lines. Use "OLD" only for deleted lines [-]. When uncertain, use "NEW".
 

package/plugin-code-critic/skills/analyze/references/level3-balanced.md

@@ -140,6 +140,15 @@ Output JSON with this structure:
   "summary": "Brief summary of how these changes connect to and impact the codebase"
 }
 
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+```suggestion
+replacement content here
+```
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
+
 ## Line Number Reference (old_or_new field)
 The "old_or_new" field indicates which line number column to use:
 - **"NEW"** (default): Use the NEW column number. This is correct for:

package/plugin-code-critic/skills/analyze/references/level3-fast.md

@@ -110,6 +110,15 @@ Output JSON with this structure:
   "summary": "Brief summary of how these changes connect to and impact the codebase"
 }
 
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+```suggestion
+replacement content here
+```
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
+
 ## Line Numbers (old_or_new)
 - **"NEW"** (default): For added lines [+] and context lines
 - **"OLD"**: Only for deleted lines [-]

package/plugin-code-critic/skills/analyze/references/level3-thorough.md

@@ -251,6 +251,15 @@ Output JSON with this structure:
   "summary": "Brief summary of how these changes connect to and impact the codebase"
 }
 
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+```suggestion
+replacement content here
+```
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
+
 ## Line Number Reference (old_or_new field)
 The "old_or_new" field indicates which line number column to use:
 - **"NEW"** (default): Use the NEW column number. This is correct for:

package/plugin-code-critic/skills/analyze/references/orchestration-balanced.md

@@ -120,6 +120,15 @@ Output JSON with this structure:
   "summary": "Brief summary of the key findings and their significance to the reviewer. Focus on WHAT was found, not HOW it was found. Do NOT mention 'orchestration', 'levels', 'merged from Level 1/2/3' etc. Write as if a single reviewer produced this analysis."
 }
 
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+```suggestion
+replacement content here
+```
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
+
 ## Line Number Reference (old_or_new field)
 The "old_or_new" field indicates which line number column to use:
 - **"NEW"** (default): Correct for ADDED lines and CONTEXT lines (unchanged lines in both versions)

package/plugin-code-critic/skills/analyze/references/orchestration-fast.md

@@ -97,6 +97,15 @@ Use "Consider...", "Worth noting..." - guidance not mandates.
   "summary": "Key findings as if from single reviewer (no mention of levels/orchestration)"
 }
 
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+```suggestion
+replacement content here
+```
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
+
 ## old_or_new
 "NEW" (default): added [+] and context lines. "OLD": deleted [-] only. Preserve from input.
 

package/plugin-code-critic/skills/analyze/references/orchestration-thorough.md

@@ -250,6 +250,15 @@ Output JSON with this structure:
   "summary": "Brief summary of the key findings and their significance to the reviewer. Focus on WHAT was found, not HOW it was found. Do NOT mention 'orchestration', 'levels', 'merged from Level 1/2/3' etc. Write as if a single reviewer produced this analysis."
 }
 
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+```suggestion
+replacement content here
+```
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
+
 ## Line Number Reference (old_or_new field)
 The "old_or_new" field indicates which line number column to use:
 - **"NEW"** (default): Use the NEW column number. This is correct for:

package/public/js/components/ChatPanel.js

@@ -2827,7 +2827,7 @@ class ChatPanel {
   _handleDismissCommentClick() {
     if (this.isStreaming || !this._contextItemId) return;
     this._pendingActionContext = { type: 'dismiss-comment', itemId: this._contextItemId };
-    this.inputEl.value = 'Please delete this comment.';
+    this.inputEl.value = 'Please dismiss this comment.';
     this.sendMessage();
   }
 

package/src/ai/analyzer.js

@@ -3505,8 +3505,12 @@ File-level suggestions should NOT have a line number. They apply to the entire f
         continue;
       }
 
+      const suggestionText = suggestion.suggestion;
+      const hasSuggestionBlock = suggestionText?.trimStart().startsWith('```suggestion');
       const body = suggestion.description +
-        (suggestion.suggestion ? '\n\n**Suggestion:** ' + suggestion.suggestion : '');
+        (suggestionText
+          ? (hasSuggestionBlock ? '\n\n' + suggestionText : '\n\n**Suggestion:** ' + suggestionText)
+          : '');
 
       const isFileLevel = suggestion.is_file_level === true || suggestion.line_start === null ? 1 : 0;
       const side = suggestion.old_or_new === 'OLD' ? 'LEFT' : 'RIGHT';

package/src/ai/prompts/baseline/consolidation/balanced.js

@@ -118,6 +118,15 @@ Output JSON with this structure:
   }],
   "summary": "Brief consolidation summary. Write as if a single reviewer produced this analysis — do NOT mention 'consolidation', 'merging', or 'multiple reviewers'."
 }
+
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+\`\`\`suggestion
+replacement content here
+\`\`\`
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
 </section>
 
 <section name="diff-instructions" required="true">

package/src/ai/prompts/baseline/consolidation/fast.js

@@ -89,6 +89,15 @@ Merge suggestions from multiple AI reviewers. Deduplicate. Resolve conflicts. Ke
   }],
   "summary": "Key findings as if from single reviewer (no mention of consolidation/merging)"
 }
+
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+\`\`\`suggestion
+replacement content here
+\`\`\`
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
 </section>
 
 <section name="diff-instructions" required="true" tier="fast">

package/src/ai/prompts/baseline/consolidation/thorough.js

@@ -173,6 +173,15 @@ Output JSON with this structure:
   }],
   "summary": "Brief summary of the key findings and their significance. Write as if a single reviewer produced this analysis — do NOT mention 'consolidation', 'merging', or 'multiple reviewers'."
 }
+
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+\`\`\`suggestion
+replacement content here
+\`\`\`
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
 </section>
 
 <section name="diff-instructions" required="true" tier="thorough">

package/src/ai/prompts/baseline/level1/balanced.js

@@ -119,6 +119,15 @@ Do NOT modify files or run write commands. Analyze and report only.
   }],
   "summary": "Brief summary of findings"
 }
+
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+\`\`\`suggestion
+replacement content here
+\`\`\`
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
 </section>
 
 <section name="diff-instructions" required="true">

package/src/ai/prompts/baseline/level1/fast.js

@@ -98,6 +98,15 @@ Annotated diff tool, \`cat -n\`, ls, find, grep. Do NOT modify files.
   }],
   "summary": "Brief summary"
 }
+
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+\`\`\`suggestion
+replacement content here
+\`\`\`
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
 </section>
 
 <section name="diff-instructions" required="true" tier="fast">

package/src/ai/prompts/baseline/level1/thorough.js

@@ -161,6 +161,15 @@ Output JSON with this structure:
   }],
   "summary": "Brief summary of findings"
 }
+
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+\`\`\`suggestion
+replacement content here
+\`\`\`
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
 </section>
 
 <section name="diff-instructions" required="true" tier="thorough">

package/src/ai/prompts/baseline/level2/balanced.js

@@ -126,6 +126,15 @@ Note: You may use parallel read-only Tasks to examine multiple files simultaneou
   }],
   "summary": "Brief summary of file context findings"
 }
+
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+\`\`\`suggestion
+replacement content here
+\`\`\`
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
 </section>
 
 <section name="diff-instructions" required="true">

package/src/ai/prompts/baseline/level2/fast.js

@@ -107,6 +107,15 @@ Annotated diff tool (preferred), \`cat -n <file>\`, ls, find, grep. Do NOT modif
   }],
   "summary": "Brief summary"
 }
+
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+\`\`\`suggestion
+replacement content here
+\`\`\`
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
 </section>
 
 <section name="diff-instructions" required="true" tier="fast">

package/src/ai/prompts/baseline/level2/thorough.js

@@ -201,6 +201,15 @@ Output JSON with this structure:
   }],
   "summary": "Brief summary of file context findings"
 }
+
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+\`\`\`suggestion
+replacement content here
+\`\`\`
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
 </section>
 
 <section name="diff-instructions" required="true" tier="thorough">

package/src/ai/prompts/baseline/level3/balanced.js

@@ -150,6 +150,15 @@ Output JSON with this structure:
   }],
   "summary": "Brief summary of how these changes connect to and impact the codebase"
 }
+
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+\`\`\`suggestion
+replacement content here
+\`\`\`
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
 </section>
 
 <section name="diff-instructions" required="true">

package/src/ai/prompts/baseline/level3/fast.js

@@ -124,6 +124,15 @@ Output JSON with this structure:
   }],
   "summary": "Brief summary of how these changes connect to and impact the codebase"
 }
+
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+\`\`\`suggestion
+replacement content here
+\`\`\`
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
 </section>
 
 <section name="diff-instructions" required="true" tier="fast">

package/src/ai/prompts/baseline/level3/thorough.js

@@ -268,6 +268,15 @@ Output JSON with this structure:
   }],
   "summary": "Brief summary of how these changes connect to and impact the codebase"
 }
+
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+\`\`\`suggestion
+replacement content here
+\`\`\`
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
 </section>
 
 <section name="diff-instructions" required="true" tier="thorough">

package/src/ai/prompts/baseline/orchestration/balanced.js

@@ -140,6 +140,15 @@ Output JSON with this structure:
   }],
   "summary": "Brief summary of the key findings and their significance to the reviewer. Focus on WHAT was found, not HOW it was found. Do NOT mention 'orchestration', 'levels', 'merged from Level 1/2/3' etc. Write as if a single reviewer produced this analysis."
 }
+
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+\`\`\`suggestion
+replacement content here
+\`\`\`
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
 </section>
 
 <section name="diff-instructions" required="true">

package/src/ai/prompts/baseline/orchestration/fast.js

@@ -120,6 +120,15 @@ Use "Consider...", "Worth noting..." - guidance not mandates.
   }],
   "summary": "Key findings as if from single reviewer (no mention of levels/orchestration)"
 }
+
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+\`\`\`suggestion
+replacement content here
+\`\`\`
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
 </section>
 
 <section name="diff-instructions" required="true" tier="fast">

package/src/ai/prompts/baseline/orchestration/thorough.js

@@ -283,6 +283,15 @@ Output JSON with this structure:
   }],
   "summary": "Brief summary of the key findings and their significance to the reviewer. Focus on WHAT was found, not HOW it was found. Do NOT mention 'orchestration', 'levels', 'merged from Level 1/2/3' etc. Write as if a single reviewer produced this analysis."
 }
+
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+\`\`\`suggestion
+replacement content here
+\`\`\`
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.
 </section>
 
 <section name="diff-instructions" required="true" tier="thorough">

package/src/ai/prompts/shared/output-schema.js

@@ -148,7 +148,16 @@ function buildOutputSchemaSection(schema) {
 Output ONLY valid JSON with no additional text, explanations, or markdown code blocks. Do not wrap the JSON in \`\`\`json blocks. The response must start with { and end with }.
 
 Output JSON with this structure:
-${JSON.stringify(schema, null, 2)}`
+${JSON.stringify(schema, null, 2)}
+
+### GitHub Suggestion Syntax
+When suggesting a specific change, **embed** a GitHub suggestion block within the "suggestion" field:
+
+\`\`\`suggestion
+replacement content here
+\`\`\`
+
+The content inside the block is the complete replacement for the commented line(s). Do not include explanation inside the block — any explanation should appear as plain text outside it. For non-specific suggestions, use plain text only.`
   };
 }
 

package/src/chat/prompt-builder.js

@@ -44,6 +44,7 @@ function buildChatPrompt({ review, prData, skillPath, chatInstructions }) {
     '- **Comments** are human-curated review findings (created by the reviewer).',
     '- **Suggestions** are AI-generated findings from analysis runs.',
     '- **Workflow**: AI generates suggestions → reviewer triages (adopt, edit, or dismiss) → adopted suggestions become comments.',
+    '- **IMPORTANT**: Do NOT adopt, dismiss, or modify suggestions or comments unless the user explicitly asks you to. Your role is to discuss and explain — the reviewer decides what action to take.',
     '- **Analysis runs** are the process that produces suggestions. Each run has a provider, model, tier, and status.',
     '- **Review ID** is a stable integer identifying this review session, used in all API calls.'
   ];
@@ -69,7 +70,11 @@ function buildChatPrompt({ review, prData, skillPath, chatInstructions }) {
     'These become clickable links in the UI. Do NOT use backtick code spans for file references you want to be clickable.\n\n' +
     'Files in the diff can be referenced freely. Files outside the diff can also be referenced; ' +
     'to make them visible in the diff panel, add them as context files via the API (see skill). ' +
-    'Add context files judiciously — only when directly relevant, with focused line ranges.'
+    'Add context files judiciously — only when directly relevant, with focused line ranges.\n\n' +
+    'When the user asks to see code (e.g. "Show me…", "Where is…", "What does X look like?"), ' +
+    'add the relevant file as a context file with a focused line range so it appears in the diff panel. ' +
+    'When explaining code, prefer referencing specific line ranges (e.g. [[file:path.js:10-25]]) ' +
+    'over quoting large blocks in your response. Short inline snippets (a few lines) are fine when they clarify the explanation.'
   );
 
   // Tool usage discipline — avoid unnecessary Task delegation

package/src/database.js

@@ -2193,8 +2193,12 @@ class CommentRepository {
     }
 
     for (const suggestion of normalized) {
+      const suggestionText = suggestion.suggestion;
+      const hasSuggestionBlock = suggestionText?.trimStart().startsWith('```suggestion');
       const body = suggestion.description +
-        (suggestion.suggestion ? '\n\n**Suggestion:** ' + suggestion.suggestion : '');
+        (suggestionText
+          ? (hasSuggestionBlock ? '\n\n' + suggestionText : '\n\n**Suggestion:** ' + suggestionText)
+          : '');
 
       // File-level suggestions have is_file_level=true or have null line_start
       const isFileLevel = suggestion.is_file_level === true || suggestion.line_start === null ? 1 : 0;

package/src/main.js

@@ -466,8 +466,6 @@ AI PROVIDERS:
  * @param {Object} flags - Parsed command line flags
  */
 async function handlePullRequest(args, config, db, flags = {}) {
-  let prInfo = null; // Declare prInfo outside try block for error handling
-  
   try {
     // Get GitHub token (env var takes precedence over config)
     const githubToken = getGitHubToken(config);
@@ -477,156 +475,36 @@ async function handlePullRequest(args, config, db, flags = {}) {
 
     // Parse PR arguments
     const parser = new PRArgumentParser();
-    prInfo = await parser.parsePRArguments(args);
-
-    console.log(`Processing pull request #${prInfo.number} from ${prInfo.owner}/${prInfo.repo}`);
-
-    // Create GitHub client and verify repository access
-    const githubClient = new GitHubClient(githubToken);
-    const repoExists = await githubClient.repositoryExists(prInfo.owner, prInfo.repo);
-    if (!repoExists) {
-      throw new Error(`Repository ${prInfo.owner}/${prInfo.repo} not found or not accessible`);
-    }
-
-    // Fetch PR data from GitHub
-    console.log('Fetching pull request data from GitHub...');
-    const prData = await githubClient.fetchPullRequest(prInfo.owner, prInfo.repo, prInfo.number);
+    const prInfo = await parser.parsePRArguments(args);
 
-    // Determine repository path: only use cwd if it matches the target repo
+    // Register cwd as known repo path if it matches the target repo
     const currentDir = parser.getCurrentDirectory();
     const isMatchingRepo = await parser.isMatchingRepository(currentDir, prInfo.owner, prInfo.repo);
-    const repository = normalizeRepository(prInfo.owner, prInfo.repo);
-
-    let repositoryPath;
-    let worktreeSourcePath;
-    let checkoutScript;
-    let checkoutTimeout;
-    let worktreeConfig = null;
     if (isMatchingRepo) {
-      // Current directory is a checkout of the target repository
-      repositoryPath = currentDir;
-      // Register the known repository location for future web UI usage
       await registerRepositoryLocation(db, currentDir, prInfo.owner, prInfo.repo);
-
-      // Resolve monorepo config options (checkout_script, worktree_directory, worktree_name_template)
-      // even when running from inside the target repo, so they are not silently ignored.
-      const resolved = resolveMonorepoOptions(config, repository);
-      checkoutScript = resolved.checkoutScript;
-      checkoutTimeout = resolved.checkoutTimeout;
-      worktreeConfig = resolved.worktreeConfig;
-    } else {
-      // Current directory is not the target repository - find or clone it
-      console.log(`Current directory is not a checkout of ${prInfo.owner}/${prInfo.repo}, locating repository...`);
-      const result = await findRepositoryPath({
-        db,
-        owner: prInfo.owner,
-        repo: prInfo.repo,
-        repository,
-        prNumber: prInfo.number,
-        config,
-        onProgress: (progress) => {
-          if (progress.message) {
-            console.log(progress.message);
-          }
-        }
-      });
-      repositoryPath = result.repositoryPath;
-      worktreeSourcePath = result.worktreeSourcePath;
-      checkoutScript = result.checkoutScript;
-      checkoutTimeout = result.checkoutTimeout;
-      worktreeConfig = result.worktreeConfig;
     }
 
-    // Setup git worktree
-    console.log('Setting up git worktree...');
-    const worktreeManager = new GitWorktreeManager(db, worktreeConfig || {});
-    const worktreePath = await worktreeManager.createWorktreeForPR(prInfo, prData, repositoryPath, {
-      worktreeSourcePath,
-      checkoutScript,
-      checkoutTimeout
-    });
-
-    // Generate unified diff
-    console.log('Generating unified diff...');
-    const diff = await worktreeManager.generateUnifiedDiff(worktreePath, prData);
-    const changedFiles = await worktreeManager.getChangedFiles(worktreePath, prData);
+    // Set model override if provided via CLI flag
+    if (flags.model) {
+      process.env.PAIR_REVIEW_MODEL = flags.model;
+    }
 
-    // Store PR data in database
-    console.log('Storing pull request data...');
-    await storePRData(db, prInfo, prData, diff, changedFiles, worktreePath);
+    // Start server and open browser to setup page
+    const port = await startServer(db);
 
-    // Start server with PR context
-    console.log('Starting server...');
-    const port = await startServerWithPRContext(config, prInfo, flags);
+    // Async cleanup of stale worktrees (don't block startup)
+    cleanupStaleWorktreesAsync(config);
 
-    // Trigger AI analysis server-side if --ai flag is present
+    let url = `http://localhost:${port}/pr/${prInfo.owner}/${prInfo.repo}/${prInfo.number}`;
     if (flags.ai) {
-      console.log('Starting AI analysis...');
-
-      // Wait for server to be ready with retry logic
-      const maxRetries = 5;
-      const retryDelay = 200; // ms
-      let lastError;
-
-      for (let attempt = 1; attempt <= maxRetries; attempt++) {
-        try {
-          // Add small delay to ensure server is fully initialized
-          if (attempt > 1) {
-            await new Promise(resolve => setTimeout(resolve, retryDelay * attempt));
-          }
-
-          const response = await fetch(`http://localhost:${port}/api/pr/${prInfo.owner}/${prInfo.repo}/${prInfo.number}/analyses`, {
-            method: 'POST',
-            headers: { 'Content-Type': 'application/json' }
-          });
-
-          if (response.ok) {
-            const result = await response.json();
-            console.log(`AI analysis started (ID: ${result.analysisId})`);
-            break; // Success, exit retry loop
-          } else {
-            lastError = `Server responded with ${response.status}: ${await response.text()}`;
-            if (attempt === maxRetries) {
-              console.warn('Failed to start AI analysis:', lastError);
-            }
-          }
-        } catch (error) {
-          lastError = error.message;
-          if (attempt === maxRetries) {
-            console.warn('Could not start AI analysis after', maxRetries, 'attempts:', lastError);
-          }
-        }
-      }
+      url += '?analyze=true';
     }
 
-    // Open browser to PR view
-    const url = `http://localhost:${port}/pr/${prInfo.owner}/${prInfo.repo}/${prInfo.number}`;
-
     console.log(`Opening browser to: ${url}`);
     await open(url);
 
   } catch (error) {
-    // Provide cleaner error messages for common issues
-    if (error.message && error.message.includes('not found in repository')) {
-      if (prInfo) {
-        console.error(`\n❌ Pull request #${prInfo.number} does not exist in ${prInfo.owner}/${prInfo.repo}`);
-      } else {
-        console.error(`\n❌ ${error.message}`);
-      }
-      console.error('Please check the PR number and try again.\n');
-    } else if (error.message && error.message.includes('authentication failed')) {
-      console.error('\n❌ GitHub authentication failed');
-      console.error('Please check your token in ~/.pair-review/config.json\n');
-    } else if (error.message && error.message.includes('Repository') && error.message.includes('not found')) {
-      console.error(`\n❌ ${error.message}`);
-      console.error('Please check the repository name and your access permissions.\n');
-    } else if (error.message && error.message.includes('Network error')) {
-      console.error('\n❌ Network connection error');
-      console.error('Please check your internet connection and try again.\n');
-    } else {
-      // For other errors, show a clean message without stack trace
-      console.error(`\n❌ Error: ${error.message}\n`);
-    }
+    console.error(`\n❌ Error: ${error.message}\n`);
     process.exit(1);
   }
 }
@@ -647,36 +525,6 @@ async function startServerOnly(config) {
   await open(url);
 }
 
-/**
- * Start server with PR context
- * @param {Object} config - Application configuration
- * @param {Object} prInfo - PR information
- * @param {Object} flags - Command line flags
- * @returns {Promise<number>} Server port
- */
-async function startServerWithPRContext(config, prInfo, flags = {}) {
-  // Set environment variable for PR context
-  process.env.PAIR_REVIEW_PR = JSON.stringify(prInfo);
-
-  // Set environment variable for auto-AI flag
-  if (flags.ai) {
-    process.env.PAIR_REVIEW_AUTO_AI = 'true';
-  }
-
-  // Set environment variable for model override (CLI takes priority)
-  if (flags.model) {
-    process.env.PAIR_REVIEW_MODEL = flags.model;
-  }
-
-  const { startServer } = require('./server');
-  const actualPort = await startServer(db);
-
-  // Async cleanup of stale worktrees (don't block startup)
-  cleanupStaleWorktreesAsync(config);
-
-  // Return the actual port the server started on
-  return actualPort;
-}
 
 /**
  * Format AI suggestion with emoji and category prefix