Threadlinking ignore modifications

Author: thrialectics

.gitignore

@@ -4,3 +4,6 @@ dist/
 .DS_Store
 /.mcp.json
 Context.md
+CHANGELOG.md
+HANDOFF-*.md
+*.jpg

Context.md

@@ -115,6 +115,7 @@ If you prefer to configure components individually instead of using `init`:
 | PostToolUse hook | Auto-tracks files you create/edit | `~/.claude/settings.json` |
 | MCP Server | Gives Claude direct tool access | `~/.claude/mcp.json` |
 | CLAUDE.md block | Teaches Claude when/how to use threadlinking | `~/.claude/CLAUDE.md` |
+| Ignore file | Filters noise from pending files | `~/.threadlinkingignore` |
 
 All components are optional and can be skipped during init.
 

README.md

@@ -3,11 +3,13 @@ import { readFileSync, writeFileSync, existsSync, mkdirSync, appendFileSync, cop
 import { homedir } from 'os';
 import { join } from 'path';
 import { createInterface } from 'readline';
+import { getDefaultIgnoreContent } from '../core/ignore.js';
 
 const CLAUDE_DIR = join(homedir(), '.claude');
 const SETTINGS_PATH = join(CLAUDE_DIR, 'settings.json');
 const MCP_JSON_PATH = join(CLAUDE_DIR, 'mcp.json');
 const CLAUDE_MD_PATH = join(CLAUDE_DIR, 'CLAUDE.md');
+const GLOBAL_IGNORE_PATH = join(homedir(), '.threadlinkingignore');
 
 const POST_TOOL_USE_HOOK_CONFIG = {
   matcher: 'Edit|Write',
@@ -86,6 +88,7 @@ interface SetupStatus {
   sessionStartHookInstalled: boolean;
   mcpConfigured: boolean;
   claudeMdPresent: boolean;
+  ignoreFilePresent: boolean;
   settingsJsonValid: boolean;
   mcpJsonValid: boolean;
 }
@@ -175,13 +178,17 @@ function checkStatus(): SetupStatus {
     claudeMdPresent = content.toLowerCase().includes('threadlinking');
   }
 
+  // Check ignore file
+  const ignoreFilePresent = existsSync(GLOBAL_IGNORE_PATH);
+
   return {
     claudeCodeDetected,
     claudeDirExists,
     postToolUseHookInstalled,
     sessionStartHookInstalled,
     mcpConfigured,
     claudeMdPresent,
+    ignoreFilePresent,
     settingsJsonValid,
     mcpJsonValid,
   };
@@ -309,6 +316,7 @@ function printStatus(status: SetupStatus): void {
   console.log(`  SessionStart hook:  ${status.sessionStartHookInstalled ? '\u2713 Installed' : '\u2717 Not installed'}`);
   console.log(`  MCP server:         ${status.mcpConfigured ? '\u2713 Configured (mcp.json)' : '\u2717 Not configured'}`);
   console.log(`  CLAUDE.md:          ${status.claudeMdPresent ? '\u2713 Present' : '\u2717 Not present'}`);
+  console.log(`  Ignore file:        ${status.ignoreFilePresent ? '\u2713 Present' : '\u2717 Not present'}`);
 
   if (!status.settingsJsonValid && existsSync(SETTINGS_PATH)) {
     console.log(`  settings.json:      \u2717 Invalid JSON`);
@@ -371,7 +379,7 @@ export const initCommand = new Command('init')
     }
 
     // Step 1: PostToolUse hook
-    console.log('[1/4] PostToolUse hook (auto-tracks files you create)');
+    console.log('[1/5] PostToolUse hook (auto-tracks files you create)');
     if (status.postToolUseHookInstalled) {
       console.log('      Status: Already installed');
       console.log('      \u2713 Skipping\n');
@@ -398,7 +406,7 @@ export const initCommand = new Command('init')
     }
 
     // Step 2: SessionStart hook
-    console.log('[2/4] SessionStart hook (shows context at session start)');
+    console.log('[2/5] SessionStart hook (shows context at session start)');
     if (status.sessionStartHookInstalled) {
       console.log('      Status: Already installed');
       console.log('      \u2713 Skipping\n');
@@ -419,7 +427,7 @@ export const initCommand = new Command('init')
     }
 
     // Step 3: MCP Server (uses separate mcp.json file)
-    console.log('[3/4] MCP Server (gives Claude direct access to threadlinking tools)');
+    console.log('[3/5] MCP Server (gives Claude direct access to threadlinking tools)');
     let { mcpJson, valid: mcpJsonValid } = loadMcpJson();
 
     // Handle invalid mcp.json
@@ -475,7 +483,7 @@ export const initCommand = new Command('init')
     }
 
     // Step 4: CLAUDE.md
-    console.log('[4/4] CLAUDE.md instructions (teaches Claude when/how to use threadlinking)');
+    console.log('[4/5] CLAUDE.md instructions (teaches Claude when/how to use threadlinking)');
     if (status.claudeMdPresent) {
       console.log('      Status: Already present');
       console.log('      \u2713 Skipping\n');
@@ -494,6 +502,26 @@ export const initCommand = new Command('init')
       }
     }
 
+    // Step 5: Ignore file
+    console.log('[5/5] Ignore file (filters noise from pending files list)');
+    if (status.ignoreFilePresent) {
+      console.log('      Status: Already present');
+      console.log('      \u2713 Skipping\n');
+    } else {
+      console.log('      Status: Not present');
+      let shouldInstall = true;
+      if (options.interactive !== false) {
+        const answer = await ask('      Create ~/.threadlinkingignore? (Y/n) ');
+        shouldInstall = answer !== 'n' && answer !== 'no';
+      }
+      if (shouldInstall) {
+        writeFileSync(GLOBAL_IGNORE_PATH, getDefaultIgnoreContent(), 'utf-8');
+        console.log('      \u2713 Ignore file created\n');
+      } else {
+        console.log('      Skipped\n');
+      }
+    }
+
     // Done
     console.log('Done! Threadlinking is fully configured.\n');
     console.log('Start a new Claude Code session to begin.');

package-lock.json

@@ -0,0 +1,28 @@
+import { Command } from 'commander';
+import { pruneIgnored } from '../core/index.js';
+
+export const pruneCommand = new Command('prune')
+  .description('Remove ignored files from the pending list')
+  .option('--verbose', 'Show each removed file')
+  .action((options) => {
+    const result = pruneIgnored();
+
+    if (!result.success) {
+      console.error(`Error: ${result.message}`);
+      process.exitCode = 1;
+      return;
+    }
+
+    console.log(result.message);
+
+    if (options.verbose && result.data && result.data.removed.length > 0) {
+      console.log('\nRemoved:');
+      for (const path of result.data.removed) {
+        console.log(`  - ${path}`);
+      }
+    }
+
+    if (result.data && result.data.remaining > 0) {
+      console.log(`\n${result.data.remaining} file${result.data.remaining > 1 ? 's' : ''} remaining in pending list.`);
+    }
+  });

src/commands/init.ts

@@ -35,7 +35,6 @@ export const reindexCommand = new Command('reindex')
       }
       process.exit(1);
     } finally {
-      // Clean up Python process
       cleanup();
     }
   });

src/commands/prune.ts

@@ -28,6 +28,7 @@ export {
   truncate,
   parseTags,
   detectProjectRoot,
+  prompt,
   MAX_SUMMARY_LENGTH,
   MAX_TAG_LENGTH,
   MAX_SNIPPET_LENGTH,

src/commands/reindex.ts

@@ -13,7 +13,6 @@ export { searchThreads } from './search.js';
 export { pruneIgnored } from './prune.js';
 export type { PruneResult } from './prune.js';
 
-// Premium operations (license required)
 export { semanticSearch } from './semantic.js';
 export { getAnalytics } from './analytics.js';
 export { exportThread } from './export.js';

src/core/index.ts

@@ -16,7 +16,6 @@ export interface Thread {
   chat_url?: string;
   date_created: string;
   date_modified?: string;
-  auto_generated?: boolean;
 }
 
 export type ThreadIndex = Record<string, Thread>;