fix: file subagent transcripts under their real project, not "subagents"

dist/db.d.ts

@@ -1,6 +1,14 @@
 import Database from 'better-sqlite3';
 import { ConversationExchange } from './types.js';
 export declare function migrateSchema(db: Database.Database): void;
+/**
+ * Earlier versions took a transcript's parent directory as its project, so
+ * every subagent transcript (<project>/<session>/subagents/agent-*.jsonl) was
+ * indexed under the project "subagents". Re-derive the project for those rows.
+ * Rows from a real project named "subagents" derive to the same name and are
+ * left as they are, so this is safe to run on every startup.
+ */
+export declare function migrateSubagentProjects(db: Database.Database): void;
 /**
  * Earlier versions created `tool_calls` with a plain
  * `FOREIGN KEY (exchange_id) REFERENCES exchanges(id)`.

dist/db.js

@@ -2,7 +2,7 @@ import Database from 'better-sqlite3';
 import path from 'path';
 import fs from 'fs';
 import * as sqliteVec from 'sqlite-vec';
-import { getDbPath } from './paths.js';
+import { getDbPath, projectFromTranscriptPath } from './paths.js';
 import { EMBEDDING_VERSION } from './embedding-migration.js';
 export function migrateSchema(db) {
     const columns = db.prepare(`SELECT name FROM pragma_table_info('exchanges')`).all();
@@ -36,6 +36,28 @@ export function migrateSchema(db) {
         console.log('Migration complete.');
     }
     migrateToolCallsCascade(db);
+    migrateSubagentProjects(db);
+}
+/**
+ * Earlier versions took a transcript's parent directory as its project, so
+ * every subagent transcript (<project>/<session>/subagents/agent-*.jsonl) was
+ * indexed under the project "subagents". Re-derive the project for those rows.
+ * Rows from a real project named "subagents" derive to the same name and are
+ * left as they are, so this is safe to run on every startup.
+ */
+export function migrateSubagentProjects(db) {
+    const rows = db.prepare(`SELECT DISTINCT archive_path FROM exchanges WHERE project = 'subagents'`).all();
+    const update = db.prepare(`UPDATE exchanges SET project = ? WHERE archive_path = ?`);
+    const fixes = rows
+        .map(r => ({ path: r.archive_path, project: projectFromTranscriptPath(r.archive_path) }))
+        .filter(f => f.project !== 'subagents');
+    if (fixes.length === 0)
+        return;
+    console.log(`Migrating ${fixes.length} subagent transcript(s) out of the "subagents" project...`);
+    db.transaction(() => {
+        for (const f of fixes)
+            update.run(f.project, f.path);
+    })();
 }
 /**
  * Earlier versions created `tool_calls` with a plain

dist/mcp-server.js

@@ -30264,6 +30264,14 @@ function ensureDir(dir) {
   }
   return dir;
 }
+function projectFromTranscriptPath(filePath) {
+  let dir = path.dirname(filePath);
+  if (path.basename(dir) === "subagents" && path.basename(filePath).startsWith("agent-")) {
+    dir = path.dirname(path.dirname(dir));
+  }
+  const name = path.basename(dir);
+  return name && name !== "." ? name : "unknown";
+}
 function getSuperpowersDir() {
   let dir;
   if (process.env.EPISODIC_MEMORY_CONFIG_DIR) {
@@ -30337,6 +30345,19 @@ function migrateSchema(db) {
     console.log("Migration complete.");
   }
   migrateToolCallsCascade(db);
+  migrateSubagentProjects(db);
+}
+function migrateSubagentProjects(db) {
+  const rows = db.prepare(
+    `SELECT DISTINCT archive_path FROM exchanges WHERE project = 'subagents'`
+  ).all();
+  const update = db.prepare(`UPDATE exchanges SET project = ? WHERE archive_path = ?`);
+  const fixes = rows.map((r) => ({ path: r.archive_path, project: projectFromTranscriptPath(r.archive_path) })).filter((f) => f.project !== "subagents");
+  if (fixes.length === 0) return;
+  console.log(`Migrating ${fixes.length} subagent transcript(s) out of the "subagents" project...`);
+  db.transaction(() => {
+    for (const f of fixes) update.run(f.project, f.path);
+  })();
 }
 function migrateToolCallsCascade(db) {
   const row = db.prepare(

dist/parser.js

@@ -1,6 +1,7 @@
 import fs from 'fs';
 import readline from 'readline';
 import path from 'path';
+import { projectFromTranscriptPath } from './paths.js';
 import crypto from 'crypto';
 async function detectConversationHarness(filePath) {
     const fileStream = fs.createReadStream(filePath);
@@ -1154,10 +1155,7 @@ async function parseCursorConversation(filePath, projectName, archivePath) {
  * Extracts project name from the file path and returns exchanges with metadata
  */
 export async function parseConversationFile(filePath) {
-    // Extract project name from path (directory name before the .jsonl file).
-    // path.dirname uses the platform's separators, so Windows paths with `\` work too.
-    const parentDir = path.basename(path.dirname(filePath));
-    const project = parentDir && parentDir !== '.' ? parentDir : 'unknown';
+    const project = projectFromTranscriptPath(filePath);
     const exchanges = await parseConversation(filePath, project, filePath);
     return {
         project,

dist/paths.d.ts

@@ -61,6 +61,14 @@ export declare function getConversationSourceDirs(only?: ConversationSourceHarne
  * inside session UUIDs (#80).
  */
 export declare function findJsonlFiles(dir: string, excludedDirNames?: ReadonlySet<string>): string[];
+/**
+ * Project name for a transcript: the directory it sits in. Claude Code keeps
+ * subagent transcripts at <project>/<session>/subagents/agent-*.jsonl, so for
+ * those the project is two directories further up. Both the directory and the
+ * agent- prefix must match, so a project that is itself named "subagents"
+ * keeps its name.
+ */
+export declare function projectFromTranscriptPath(filePath: string): string;
 /**
  * statSync that follows symlinks but returns null instead of throwing when
  * the entry cannot be stat'ed — a dangling symlink (e.g. left behind by a

dist/paths.js

@@ -138,6 +138,21 @@ export function findJsonlFiles(dir, excludedDirNames) {
     }
     return results;
 }
+/**
+ * Project name for a transcript: the directory it sits in. Claude Code keeps
+ * subagent transcripts at <project>/<session>/subagents/agent-*.jsonl, so for
+ * those the project is two directories further up. Both the directory and the
+ * agent- prefix must match, so a project that is itself named "subagents"
+ * keeps its name.
+ */
+export function projectFromTranscriptPath(filePath) {
+    let dir = path.dirname(filePath);
+    if (path.basename(dir) === 'subagents' && path.basename(filePath).startsWith('agent-')) {
+        dir = path.dirname(path.dirname(dir));
+    }
+    const name = path.basename(dir);
+    return name && name !== '.' ? name : 'unknown';
+}
 /**
  * statSync that follows symlinks but returns null instead of throwing when
  * the entry cannot be stat'ed — a dangling symlink (e.g. left behind by a

dist/sync.js

@@ -2,7 +2,7 @@ import fs from 'fs';
 import path from 'path';
 import { StringDecoder } from 'string_decoder';
 import { SUMMARIZER_CONTEXT_MARKER } from './constants.js';
-import { getExcludedProjects, findJsonlFiles, statIfExists } from './paths.js';
+import { getExcludedProjects, findJsonlFiles, statIfExists, projectFromTranscriptPath } from './paths.js';
 import { formatErrorSentinel, shouldQueueForSummary } from './summary-sentinel.js';
 import { getMaxMessageBytes, isOversizeExchange } from './message-size.js';
 const EXCLUSION_MARKERS = [
@@ -271,7 +271,7 @@ export async function syncConversations(sourceDir, destDir, options = {}) {
                     // every exchange on every sync (#152). Ported from indexer.ts.
                     const hw = db.prepare('SELECT COALESCE(MAX(line_end), 0) as maxLine FROM exchanges WHERE archive_path = ?').get(file);
                     const maxIndexedLine = hw.maxLine;
-                    const project = path.basename(path.dirname(file));
+                    const project = projectFromTranscriptPath(file);
                     const exchanges = await parseConversation(file, project, file);
                     const newExchanges = maxIndexedLine > 0
                         ? exchanges.filter(e => e.lineStart > maxIndexedLine)
@@ -334,7 +334,7 @@ export async function syncConversations(sourceDir, destDir, options = {}) {
                 continue;
             }
             try {
-                const project = path.basename(path.dirname(filePath));
+                const project = projectFromTranscriptPath(filePath);
                 const exchanges = await parseConversation(filePath, project, filePath);
                 if (exchanges.length === 0) {
                     // Skip empty conversations — write an empty -summary.txt sentinel so they aren't re-queued forever

src/db.ts

@@ -3,7 +3,7 @@ import { ConversationExchange } from './types.js';
 import path from 'path';
 import fs from 'fs';
 import * as sqliteVec from 'sqlite-vec';
-import { getDbPath } from './paths.js';
+import { getDbPath, projectFromTranscriptPath } from './paths.js';
 import { EMBEDDING_VERSION } from './embedding-migration.js';
 
 export function migrateSchema(db: Database.Database): void {
@@ -42,6 +42,30 @@ export function migrateSchema(db: Database.Database): void {
   }
 
   migrateToolCallsCascade(db);
+  migrateSubagentProjects(db);
+}
+
+/**
+ * Earlier versions took a transcript's parent directory as its project, so
+ * every subagent transcript (<project>/<session>/subagents/agent-*.jsonl) was
+ * indexed under the project "subagents". Re-derive the project for those rows.
+ * Rows from a real project named "subagents" derive to the same name and are
+ * left as they are, so this is safe to run on every startup.
+ */
+export function migrateSubagentProjects(db: Database.Database): void {
+  const rows = db.prepare(
+    `SELECT DISTINCT archive_path FROM exchanges WHERE project = 'subagents'`
+  ).all() as Array<{ archive_path: string }>;
+  const update = db.prepare(`UPDATE exchanges SET project = ? WHERE archive_path = ?`);
+  const fixes = rows
+    .map(r => ({ path: r.archive_path, project: projectFromTranscriptPath(r.archive_path) }))
+    .filter(f => f.project !== 'subagents');
+  if (fixes.length === 0) return;
+
+  console.log(`Migrating ${fixes.length} subagent transcript(s) out of the "subagents" project...`);
+  db.transaction(() => {
+    for (const f of fixes) update.run(f.project, f.path);
+  })();
 }
 
 /**

src/parser.ts

@@ -2,6 +2,7 @@ import fs from 'fs';
 import readline from 'readline';
 import path from 'path';
 import { ConversationExchange, ConversationHarness, ToolCall } from './types.js';
+import { projectFromTranscriptPath } from './paths.js';
 import crypto from 'crypto';
 
 interface JSONLMessage {
@@ -1384,11 +1385,7 @@ export async function parseConversationFile(filePath: string): Promise<{
   project: string;
   exchanges: ConversationExchange[];
 }> {
-  // Extract project name from path (directory name before the .jsonl file).
-  // path.dirname uses the platform's separators, so Windows paths with `\` work too.
-  const parentDir = path.basename(path.dirname(filePath));
-  const project = parentDir && parentDir !== '.' ? parentDir : 'unknown';
-
+  const project = projectFromTranscriptPath(filePath);
   const exchanges = await parseConversation(filePath, project, filePath);
 
   return {

src/paths.ts

@@ -150,6 +150,22 @@ export function findJsonlFiles(dir: string, excludedDirNames?: ReadonlySet<strin
   return results;
 }
 
+/**
+ * Project name for a transcript: the directory it sits in. Claude Code keeps
+ * subagent transcripts at <project>/<session>/subagents/agent-*.jsonl, so for
+ * those the project is two directories further up. Both the directory and the
+ * agent- prefix must match, so a project that is itself named "subagents"
+ * keeps its name.
+ */
+export function projectFromTranscriptPath(filePath: string): string {
+  let dir = path.dirname(filePath);
+  if (path.basename(dir) === 'subagents' && path.basename(filePath).startsWith('agent-')) {
+    dir = path.dirname(path.dirname(dir));
+  }
+  const name = path.basename(dir);
+  return name && name !== '.' ? name : 'unknown';
+}
+
 /**
  * statSync that follows symlinks but returns null instead of throwing when
  * the entry cannot be stat'ed — a dangling symlink (e.g. left behind by a

src/sync.ts

@@ -2,7 +2,7 @@ import fs from 'fs';
 import path from 'path';
 import { StringDecoder } from 'string_decoder';
 import { SUMMARIZER_CONTEXT_MARKER } from './constants.js';
-import { getExcludedProjects, findJsonlFiles, statIfExists } from './paths.js';
+import { getExcludedProjects, findJsonlFiles, statIfExists, projectFromTranscriptPath } from './paths.js';
 import { formatErrorSentinel, shouldQueueForSummary } from './summary-sentinel.js';
 import { getMaxMessageBytes, isOversizeExchange } from './message-size.js';
 
@@ -309,7 +309,7 @@ export async function syncConversations(
           ).get(file) as { maxLine: number };
           const maxIndexedLine = hw.maxLine;
 
-          const project = path.basename(path.dirname(file));
+          const project = projectFromTranscriptPath(file);
           const exchanges = await parseConversation(file, project, file);
           const newExchanges = maxIndexedLine > 0
             ? exchanges.filter(e => e.lineStart > maxIndexedLine)
@@ -384,7 +384,7 @@ export async function syncConversations(
       }
 
       try {
-        const project = path.basename(path.dirname(filePath));
+        const project = projectFromTranscriptPath(filePath);
         const exchanges = await parseConversation(filePath, project, filePath);
 
         if (exchanges.length === 0) {