fix(indexer): derive project_path from message cwd instead of slug decoding

The old slug-to-path conversion (replace hyphens with slashes) was
  lossy and wrong for paths containing hyphens. Now infers project_path
  from the most-frequent observed cwd across session messages, falling
  back to slug decoding only when no cwd data exists. Adds
  refreshSessionProjectPaths() to backfill existing sessions on rebuild.

references/retrieval-semantics.md

@@ -30,7 +30,7 @@ Project-like fields are distinct:
 
 - `sessions.project`: stored Claude Code project slug.
 - `memories.project`: stored project slug copied onto registered memory records.
-- `sessions.project_path`: reconstructed absolute project path.
+- `sessions.project_path`: absolute session path derived from message `cwd` when available; slug decoding is only a fallback.
 - `messages.cwd`: working directory at message time.
 - helper `project`: SQL `LIKE` over `sessions.project`, not exact membership.
 

references/schema.md

@@ -17,8 +17,8 @@ One row per Claude Code session.
 CREATE TABLE sessions (
   id            TEXT PRIMARY KEY,   -- session UUID (matches JSONL filename)
   title         TEXT,               -- AI-generated session title (may be NULL)
-  project       TEXT,               -- project slug (hyphenated path, e.g. "Users-tomiya-Code-quiet-zero")
+  project       TEXT,               -- Claude project slug (e.g. "-Users-tomiya-Code-quiet-zero")
-  project_path  TEXT,               -- reconstructed filesystem path (e.g. "/Users/tomiya/Code/quiet-zero")
+  project_path  TEXT,               -- absolute session cwd-derived path, with slug fallback (e.g. "/Users/tomiya/Code/quiet-zero")
   started_at    TEXT,               -- ISO 8601 timestamp of first message
   ended_at      TEXT,               -- ISO 8601 timestamp of last message
   git_branch    TEXT,               -- git branch active during session (if any)
@@ -242,10 +242,11 @@ Full-text search across all message text using FTS5.
 | `opts.cwd` | `string` | Filter by working directory (supports LIKE) |
 
 **Scope note:** `sessions.project` is the stored Claude Code project slug,
-`sessions.project_path` is the reconstructed absolute project path, and
+`sessions.project_path` is the absolute session path derived from message `cwd`
-`messages.cwd` is the working directory at message time. Helper `project`
+when available, and `messages.cwd` is the working directory at message time.
-filters are fuzzy `LIKE` filters over `sessions.project`. For exact project
+Helper `project` filters are fuzzy `LIKE` filters over `sessions.project`. For
-membership, use `sql()` with `s.project = ?` or `s.project_path = ?`.
+exact project membership, use `sql()` with `s.project = ?` or
+`s.project_path = ?`.
 
 **Returns:** `Array<{ message, session, rank, context }>` where `context` is the
 6 nearest messages by timestamp in the same session. It is temporal neighbor

scripts/indexer.mjs

@@ -3,6 +3,29 @@ import { CLAUDE_DIR, openDb, trunc, truncJson, extractText, filePath, isDir, rea
 const PROJECTS_DIR = path.join(CLAUDE_DIR, 'projects');
 const HISTORY_PATH = path.join(CLAUDE_DIR, 'history.jsonl');
 
+function legacyProjectPathFromSlug(project) {
+  if (!project) return null;
+  return '/' + project.replace(/-/g, '/').replace(/^\//, '');
+}
+
+function normalizeObservedCwd(cwd) {
+  if (typeof cwd !== 'string' || !cwd.trim() || !path.isAbsolute(cwd)) return null;
+  return path.normalize(cwd);
+}
+
+function inferProjectPath(project, observedCwds = []) {
+  const byPath = new Map();
+  for (const cwd of observedCwds) {
+    const normalized = normalizeObservedCwd(cwd);
+    if (!normalized) continue;
+    const current = byPath.get(normalized) || { path: normalized, count: 0, first: byPath.size };
+    current.count++;
+    byPath.set(normalized, current);
+  }
+  const best = [...byPath.values()].sort((a, b) => b.count - a.count || a.first - b.first)[0];
+  return best?.path || legacyProjectPathFromSlug(project);
+}
+
 function discoverJsonlFiles() {
   const files = [];
   if (!fs.existsSync(PROJECTS_DIR)) return files;
@@ -74,6 +97,7 @@ function indexJsonl(db, fi) {
     version: existing?.version || null,
     title: existing?.title || null,
     n: existing?.message_count || 0,
+    cwds: [],
   };
 
   let lineNum = 0;
@@ -101,6 +125,7 @@ function indexJsonl(db, fi) {
     if (obj.gitBranch) sm.git_branch = obj.gitBranch;
     if (obj.version) sm.version = obj.version;
     sm.n++;
+    if (!fi.isSubagent && obj.cwd) sm.cwds.push(obj.cwd);
 
     const msg = obj.message || {};
     const text = extractText(msg.content);
@@ -132,12 +157,28 @@ function indexJsonl(db, fi) {
   });
 
   if (!fi.isSubagent) {
-    const pp = '/' + fi.project.replace(/-/g, '/').replace(/^\//, '');
+    const pp = inferProjectPath(fi.project, sm.cwds);
     ins.ses.run(fi.sessionId, sm.title, fi.project, pp, sm.started_at, sm.ended_at, sm.git_branch, sm.version, sm.n, fi.path);
   }
   ins.idx.run(fi.path, mt, lineNum);
 }
 
+function refreshSessionProjectPaths(db) {
+  const sessions = db.prepare('SELECT id, project FROM sessions').all();
+  const cwdStmt = db.prepare(`
+    SELECT cwd
+    FROM messages
+    WHERE session_id = ? AND cwd IS NOT NULL AND cwd != ''
+    ORDER BY timestamp IS NULL, timestamp
+  `);
+  const update = db.prepare('UPDATE sessions SET project_path = ? WHERE id = ?');
+  for (const session of sessions) {
+    const cwds = cwdStmt.all(session.id).map(row => row.cwd);
+    const projectPath = inferProjectPath(session.project, cwds);
+    if (projectPath) update.run(projectPath, session.id);
+  }
+}
+
 function indexSubagentMeta(db, fi) {
   if (!fi.isSubagent) return;
   const mp = fi.path.replace('.jsonl', '.meta.json');
@@ -226,6 +267,7 @@ function buildIndex({ force = false } = {}) {
   db.exec('BEGIN');
   try {
     indexWorkflows(db);
+    refreshSessionProjectPaths(db);
     indexHistory(db);
     db.exec("INSERT INTO messages_fts(messages_fts) VALUES('rebuild')");
     db.prepare("INSERT OR REPLACE INTO index_state (jsonl_path, mtime, lines_processed) VALUES ('__last_build__', ?, 0)").run(Date.now());
@@ -237,4 +279,4 @@ function buildIndex({ force = false } = {}) {
   db.close();
 }
 
-export { buildIndex };
+export { buildIndex, inferProjectPath, refreshSessionProjectPaths };