fix: address PR review feedback — path safety, SQL injection, gate scoping

- Resolve relative filePath against input.cwd before statSync; early-return on ENOENT
- Replace LIKE '%path%' with exact json_each equality to prevent false matches
- Sanitize and parameterize LIMIT to prevent NaN SQL errors
- Fix day-sorting to use earliest epoch in group, not first (specificity-sorted) item
- Use exact path equality in deduplicateObservations instead of substring includes
- Scope FileReadGate by session+cwd to prevent worktree collisions
- Refresh lastAccess TTL on active sessions; throttle prune to every 50 calls
- Type params as (string | number)[] instead of any[]
- Remove unused permissionDecision fields from HookResult

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

src/cli/handlers/file-context.ts

@@ -89,7 +89,8 @@ function deduplicateObservations(
     const filesRead = parseJsonArray(obs.files_read);
     const filesModified = parseJsonArray(obs.files_modified);
     const totalFiles = filesRead.length + filesModified.length;
-    const inModified = filesModified.some(f => f.includes(targetPath) || targetPath.includes(f));
+    const normalizedTarget = targetPath.replace(/\\/g, '/');
+    const inModified = filesModified.some(f => f.replace(/\\/g, '/') === normalizedTarget);
 
     let specificityScore = 0;
     if (inModified) specificityScore += 2;
@@ -117,10 +118,10 @@ function formatFileTimeline(observations: ObservationRow[], filePath: string): s
     byDay.get(day)!.push(obs);
   }
 
-  // Sort days chronologically
+  // Sort days chronologically (use earliest observation in each group, not first — which is specificity-sorted)
   const sortedDays = Array.from(byDay.entries()).sort((a, b) => {
-    const aEpoch = a[1][0].created_at_epoch;
-    const bEpoch = b[1][0].created_at_epoch;
+    const aEpoch = Math.min(...a[1].map(o => o.created_at_epoch));
+    const bEpoch = Math.min(...b[1].map(o => o.created_at_epoch));
     return aEpoch - bEpoch;
   });
 
@@ -154,12 +155,16 @@ export const fileContextHandler: EventHandler = {
     // Skip gate for files below the token-economics threshold — timeline (~370 tokens)
     // costs more than reading small files directly.
     try {
-      const stat = statSync(filePath);
+      const statPath = path.isAbsolute(filePath)
+        ? filePath
+        : path.resolve(input.cwd || process.cwd(), filePath);
+      const stat = statSync(statPath);
       if (stat.size < FILE_READ_GATE_MIN_BYTES) {
         return { continue: true, suppressOutput: true };
       }
-    } catch {
-      // File not found, symlink error, permission denied — fall through and let gate proceed
+    } catch (err: any) {
+      if (err.code === 'ENOENT') return { continue: true, suppressOutput: true };
+      // Other errors (symlink, permission denied) — fall through and let gate proceed
     }
 
     // Check if project is excluded from tracking
@@ -211,7 +216,7 @@ export const fileContextHandler: EventHandler = {
       const gateResponse = await workerHttpRequest('/api/file-context/gate', {
         method: 'POST',
         headers: { 'Content-Type': 'application/json' },
-        body: JSON.stringify({ sessionId: input.sessionId, filePath: relativePath }),
+        body: JSON.stringify({ sessionId: input.sessionId, filePath: relativePath, cwd }),
       });
 
       if (gateResponse.ok) {

src/cli/types.ts

@@ -20,8 +20,6 @@ export interface HookResult {
   hookSpecificOutput?: {
     hookEventName: string;
     additionalContext: string;
-    permissionDecision?: string;
-    permissionDecisionReason?: string;
   };
   systemMessage?: string;
   exitCode?: number;

src/services/sqlite/observations/get.ts

@@ -121,9 +121,11 @@ export function getObservationsByFilePath(
   filePath: string,
   options?: { projects?: string[]; limit?: number }
 ): ObservationRecord[] {
-  const likePattern = `%${filePath}%`;
-  const limit = options?.limit ?? 15;
-  const params: any[] = [likePattern, likePattern];
+  const rawLimit = options?.limit;
+  const limit = Number.isInteger(rawLimit) && rawLimit! > 0
+    ? Math.min(rawLimit!, 100)
+    : 15;
+  const params: (string | number)[] = [filePath, filePath];
 
   let projectClause = '';
   if (options?.projects?.length) {
@@ -132,16 +134,18 @@ export function getObservationsByFilePath(
     params.push(...options.projects);
   }
 
+  params.push(limit);
+
   const stmt = db.prepare(`
     SELECT *
     FROM observations
     WHERE (
-      EXISTS (SELECT 1 FROM json_each(files_read) WHERE value LIKE ?)
-      OR EXISTS (SELECT 1 FROM json_each(files_modified) WHERE value LIKE ?)
+      EXISTS (SELECT 1 FROM json_each(files_read) WHERE value = ?)
+      OR EXISTS (SELECT 1 FROM json_each(files_modified) WHERE value = ?)
     )
     ${projectClause}
     ORDER BY created_at_epoch DESC
-    LIMIT ${limit}
+    LIMIT ?
   `);
 
   return stmt.all(...params) as ObservationRecord[];

src/services/worker/FileReadGate.ts

@@ -3,45 +3,65 @@
  *
  * In-memory session-scoped gate tracking which files have had their timeline
  * injected. Prevents duplicate timeline injections within the same session.
+ * Keys include cwd to prevent worktree collisions.
  */
 
 interface SessionEntry {
   files: Set<string>;
-  createdAt: number;
+  lastAccess: number;
 }
 
 const TTL_MS = 4 * 60 * 60 * 1000; // 4 hours
 
 const sessionGates = new Map<string, SessionEntry>();
 
+let pruneCallCount = 0;
+const PRUNE_EVERY_N_CALLS = 50;
+
 /**
  * Lazily prune session entries older than the TTL.
+ * Throttled to run every N calls to avoid iterating all sessions on every check.
  */
 function pruneExpiredSessions(): void {
+  pruneCallCount++;
+  if (pruneCallCount < PRUNE_EVERY_N_CALLS) return;
+  pruneCallCount = 0;
+
   const now = Date.now();
-  for (const [sessionId, entry] of sessionGates) {
-    if (now - entry.createdAt > TTL_MS) {
-      sessionGates.delete(sessionId);
+  for (const [key, entry] of sessionGates) {
+    if (now - entry.lastAccess > TTL_MS) {
+      sessionGates.delete(key);
     }
   }
 }
 
 /**
- * Check if this is the first read of a file in a session, and mark it if so.
+ * Build a composite key scoped to session + cwd to prevent worktree collisions.
+ */
+function makeKey(sessionId: string, cwd?: string): string {
+  return cwd ? `${sessionId}::${cwd}` : sessionId;
+}
+
+/**
+ * Check if this is the first read of a file in a session+cwd scope, and mark it if so.
  * Returns true if this is the first attempt (file was not previously seen).
  * Returns false if the file was already seen in this session.
  */
-export function checkAndMark(sessionId: string, filePath: string): boolean {
+export function checkAndMark(sessionId: string, filePath: string, cwd?: string): boolean {
   pruneExpiredSessions();
 
+  const key = makeKey(sessionId, cwd);
   const normalizedPath = filePath.replace(/\\/g, '/');
 
-  let entry = sessionGates.get(sessionId);
+  let entry = sessionGates.get(key);
   if (!entry) {
-    entry = { files: new Set(), createdAt: Date.now() };
-    sessionGates.set(sessionId, entry);
+    entry = { files: new Set(), lastAccess: Date.now() };
+    sessionGates.set(key, entry);
   }
 
+  // Refresh TTL on every access so active sessions don't get re-blocked
+  entry.lastAccess = Date.now();
+
   if (entry.files.has(normalizedPath)) {
     return false;
   }
@@ -52,7 +72,12 @@ export function checkAndMark(sessionId: string, filePath: string): boolean {
 
 /**
  * Clear all tracked files for a session (e.g., on session end).
+ * Clears all cwd scopes for the given session.
  */
 export function clearSession(sessionId: string): void {
-  sessionGates.delete(sessionId);
+  for (const key of sessionGates.keys()) {
+    if (key === sessionId || key.startsWith(`${sessionId}::`)) {
+      sessionGates.delete(key);
+    }
+  }
 }

src/services/worker/http/routes/DataRoutes.ts

@@ -127,7 +127,8 @@ export class DataRoutes extends BaseRouteHandler {
 
     const projectsParam = req.query.projects as string | undefined;
     const projects = projectsParam ? projectsParam.split(',').filter(Boolean) : undefined;
-    const limit = req.query.limit ? parseInt(req.query.limit as string, 10) : undefined;
+    const parsedLimit = req.query.limit ? parseInt(req.query.limit as string, 10) : undefined;
+    const limit = Number.isFinite(parsedLimit) && parsedLimit! > 0 ? parsedLimit : undefined;
 
     const db = this.dbManager.getSessionStore().db;
     const observations = getObservationsByFilePath(db, filePath, { projects, limit });
@@ -508,12 +509,12 @@ export class DataRoutes extends BaseRouteHandler {
    * Returns: { firstAttempt: boolean }
    */
   private handleFileContextGate = this.wrapHandler((req: Request, res: Response): void => {
-    const { sessionId, filePath } = req.body;
+    const { sessionId, filePath, cwd } = req.body;
     if (!sessionId || !filePath) {
       this.badRequest(res, 'sessionId and filePath are required');
       return;
     }
-    const firstAttempt = checkAndMark(sessionId, filePath);
+    const firstAttempt = checkAndMark(sessionId, filePath, cwd);
     res.json({ firstAttempt });
   });
 }