@wrongstack/tools 0.273.1 → 0.275.0

package/dist/circuit-breaker.js

@@ -156,6 +156,7 @@ var CircuitBreaker = class {
     if (this.state === "open") return;
     this.state = "open";
     this.openedAt = Date.now();
+    this.window = [];
     try {
       this.onTrip?.();
     } catch {

package/dist/circuit-breaker.js.map

@@ -1 +1 @@
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Tripping on consecutive failures (models that keep repeating the\n *     same failing command, e.g. `npm install` with wrong args in a loop)\n *   - Tripping on slow call ratio (too many long-running commands suggest\n *     a hung subprocess that the model doesn't know how to kill)\n *   - Rate-limiting bursts (rapid succession of commands without reading\n *     output suggests the model isn't processing results)\n *   - Auto-recovering after a cooldown period so a fixed model can resume\n *\n * The breaker is owned by the ProcessRegistry so any tool that registers\n * a process participates in the same circuit. \"Per-tool\" isolation is\n * intentionally NOT implemented — the model treats bash/exec as one\n * resource pool; isolating them would let the model route around the\n * breaker by alternating which tool it uses.\n */\n\nexport interface CircuitBreakerConfig {\n  /**\n   * Consecutive failures before trip. Default: 5.\n   * A single success resets this counter to 0.\n   */\n  maxConsecutiveFailures?: number | undefined;\n  /**\n   * Slow-call threshold in ms. A call that runs longer than this is\n   * counted as \"slow\". Default: 60_000 (1 minute).\n   */\n  slowCallThresholdMs?: number | undefined;\n  /**\n   * Max slow calls before trip (within the sliding window). Default: 3.\n   */\n  maxSlowCalls?: number | undefined;\n  /**\n   * Sliding window for rate-limit and slow-call counting, in ms.\n   * Default: 60_000 (1 minute).\n   */\n  windowMs?: number | undefined;\n  /**\n   * Max calls within the sliding window. Default: 30.\n   * Burst exceeding this trips the breaker immediately.\n   */\n  maxCallsPerWindow?: number | undefined;\n  /**\n   * Cooldown before auto-recovery attempt, in ms. Default: 30_000 (30s).\n   * After this the breaker enters \"half-open\" state and allows one call\n   * through to test whether the problem is resolved.\n   */\n  cooldownMs?: number | undefined;\n}\n\ninterface CallRecord {\n  at: number;\n  /** True if the call threw or returned an is_error result. */\n  failed: boolean;\n  /** True if elapsed time exceeded slowCallThresholdMs. */\n  slow: boolean;\n}\n\ntype BreakerState = 'closed' | 'open' | 'half-open';\n\nconst DEFAULT_MAX_CONSECUTIVE_FAILURES = 5;\nconst DEFAULT_SLOW_CALL_THRESHOLD_MS = 180_000;\n// 3 minutes — balanced against the 5-minute bash timeout. Commands\n// running <3min are normal; 3-5min are \"slow\" and count toward the\n// breaker. 3 consecutive slow calls trip the circuit.\nconst DEFAULT_MAX_SLOW_CALLS = 3;\nconst DEFAULT_WINDOW_MS = 60_000;\nconst DEFAULT_MAX_CALLS_PER_WINDOW = 30;\nconst DEFAULT_COOLDOWN_MS = 30_000;\n\nexport interface CircuitBreakerSnapshot {\n  state: 'closed' | 'open' | 'half-open';\n  consecutiveFailures: number;\n  slowCallsInWindow: number;\n  callsInWindow: number;\n  windowMs: number;\n  cooldownRemainingMs: number | null;\n  lastFailureAt: number | null;\n  lastSlowAt: number | null;\n}\n\nexport class CircuitBreaker {\n  private readonly maxConsecutiveFailures: number;\n  private readonly slowCallThresholdMs: number;\n  private readonly maxSlowCalls: number;\n  private readonly windowMs: number;\n  private readonly maxCallsPerWindow: number;\n  private readonly cooldownMs: number;\n\n  private state: BreakerState = 'closed';\n  private consecutiveFailures = 0;\n  private window: CallRecord[] = [];\n  private lastFailureAt: number | null = null;\n  private lastSlowAt: number | null = null;\n  /** Timestamp when the breaker was opened (for cooldown calculation). */\n  private openedAt: number | null = null;\n\n  /**\n   * Master enable flag. When false the breaker is bypassed: `beforeCall`\n   * always returns true and `afterCall` records nothing. The class itself\n   * defaults to enabled (so the standalone unit tests exercise tripping); the\n   * ProcessRegistry flips this off until the user opts in via `/settings`.\n   */\n  private enabled = true;\n\n  /**\n   * Fired (best-effort) when the breaker transitions into the `open` state.\n   * The registry uses this to arm its auto kill/reset countdown.\n   */\n  onTrip?: (() => void) | undefined;\n  /**\n   * Fired (best-effort) when the breaker returns to `closed` after having been\n   * open/half-open. The registry uses this to cancel a pending kill/reset.\n   */\n  onReset?: (() => void) | undefined;\n\n  constructor(config: CircuitBreakerConfig = {}) {\n    this.maxConsecutiveFailures = config.maxConsecutiveFailures ?? DEFAULT_MAX_CONSECUTIVE_FAILURES;\n    this.slowCallThresholdMs = config.slowCallThresholdMs ?? DEFAULT_SLOW_CALL_THRESHOLD_MS;\n    this.maxSlowCalls = config.maxSlowCalls ?? DEFAULT_MAX_SLOW_CALLS;\n    this.windowMs = config.windowMs ?? DEFAULT_WINDOW_MS;\n    this.maxCallsPerWindow = config.maxCallsPerWindow ?? DEFAULT_MAX_CALLS_PER_WINDOW;\n    this.cooldownMs = config.cooldownMs ?? DEFAULT_COOLDOWN_MS;\n  }\n\n  /** Toggle the master enable. Disabling resets to a clean `closed` state. */\n  setEnabled(enabled: boolean): void {\n    if (this.enabled === enabled) return;\n    this.enabled = enabled;\n    if (!enabled) this._reset();\n  }\n\n  get isEnabled(): boolean {\n    return this.enabled;\n  }\n\n  /**\n   * Returns true if the circuit allows a new call to proceed.\n   * When false, callers should abort the tool call and return a\n   * circuit-breaker error instead of spawning a process.\n   */\n  get canProceed(): boolean {\n    if (!this.enabled) return true;\n    this._checkStateTransition();\n    return this.state !== 'open';\n  }\n\n  /**\n   * Snapshot of the current breaker state for observability (`/kill`).\n   */\n  snapshot(): CircuitBreakerSnapshot {\n    this._checkStateTransition();\n    const now = Date.now();\n    let cooldownRemaining: number | null = null;\n    if (this.openedAt !== null && this.state === 'open') {\n      const elapsed = now - this.openedAt;\n      cooldownRemaining = Math.max(0, this.cooldownMs - elapsed);\n    }\n    return {\n      state: this.state,\n      consecutiveFailures: this.consecutiveFailures,\n      slowCallsInWindow: this.window.filter((c) => c.slow).length,\n      callsInWindow: this.window.length,\n      windowMs: this.windowMs,\n      cooldownRemainingMs: cooldownRemaining,\n      lastFailureAt: this.lastFailureAt,\n      lastSlowAt: this.lastSlowAt,\n    };\n  }\n\n  /**\n   * Call this BEFORE spawning a bash/exec process.\n   * Returns true if the call is allowed; false if the breaker is open.\n   * When false, callers MUST NOT spawn a process.\n   *\n   * @param bypass - If true, skip the circuit breaker check entirely.\n   *                  Use for background/fire-and-forget processes that should\n   *                  not affect breaker state.\n   */\n  beforeCall(bypass = false): boolean {\n    if (bypass || !this.enabled) return true;\n    this._checkStateTransition();\n    if (this.state === 'open') return false;\n    return true;\n  }\n\n  /**\n   * Call this AFTER a bash/exec process finishes (success or failure).\n   * `durationMs` is the wall-clock time the process ran.\n   * `failed` is true when the process returned a non-zero exit code or\n   * threw an exception before spawning.\n   *\n   * @param bypass - If true, do not update breaker state.\n   *                  Use for background/fire-and-forget processes.\n   */\n  afterCall(durationMs: number, failed: boolean, bypass = false): void {\n    if (bypass || !this.enabled) return;\n\n    const now = Date.now();\n\n    if (this.state === 'half-open') {\n      // First call through after cooldown — if it failed, go back to open.\n      if (failed) {\n        this._trip();\n        return;\n      }\n      // Success in half-open → reset to closed.\n      this._reset();\n      return;\n    }\n\n    // Prune old records outside the sliding window.\n    this._pruneWindow(now);\n\n    const slow = durationMs >= this.slowCallThresholdMs;\n    this.window.push({ at: now, failed, slow });\n\n    if (failed) {\n      this.consecutiveFailures++;\n      this.lastFailureAt = now;\n      if (this.consecutiveFailures >= this.maxConsecutiveFailures) {\n        this._trip();\n      }\n      return;\n    }\n\n    // Success: reset consecutive failure counter.\n    this.consecutiveFailures = 0;\n\n    if (slow) {\n      this.lastSlowAt = now;\n      const slowCount = this.window.filter((c) => c.slow).length;\n      if (slowCount >= this.maxSlowCalls) {\n        this._trip();\n      }\n    }\n\n    const callCount = this.window.length;\n    if (callCount >= this.maxCallsPerWindow) {\n      // Rate limit exceeded. This is a soft trip — we reset the window\n      // and let the next call try immediately (the caller will still see\n      // canProceed=false until the window drains naturally).\n      this._trip();\n    }\n  }\n\n  /** Force the breaker open. Used by /kill force and Ctrl+C. */\n  forceOpen(): void {\n    this._trip();\n  }\n\n  /** Force a reset to closed. Used by tests and /kill reset. */\n  forceReset(): void {\n    this._reset();\n  }\n\n  private _trip(): void {\n    if (this.state === 'open') return; // already open\n    this.state = 'open';\n    this.openedAt = Date.now();\n    // Best-effort: never let a listener failure corrupt breaker state.\n    try {\n      this.onTrip?.();\n    } catch {\n      /* ignored — observability hook only */\n    }\n  }\n\n  private _reset(): void {\n    const wasRecovering = this.state !== 'closed';\n    this.state = 'closed';\n    this.consecutiveFailures = 0;\n    this.window = [];\n    this.openedAt = null;\n    // Only notify on a real recovery (open/half-open → closed), not on the\n    // initial closed state or an idempotent re-reset.\n    if (wasRecovering) {\n      try {\n        this.onReset?.();\n      } catch {\n        /* ignored — observability hook only */\n      }\n    }\n  }\n\n  /** Transition from open → half-open when cooldown elapses. */\n  private _checkStateTransition(): void {\n    if (this.state !== 'open' || this.openedAt === null) return;\n    const elapsed = Date.now() - this.openedAt;\n    if (elapsed >= this.cooldownMs) {\n      this.state = 'half-open';\n      this.openedAt = null;\n    }\n  }\n\n  private _pruneWindow(now: number): void {\n    const cutoff = now - this.windowMs;\n    this.window = this.window.filter((c) => c.at >= cutoff);\n  }\n}"]}
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Tripping on consecutive failures (models that keep repeating the\n *     same failing command, e.g. `npm install` with wrong args in a loop)\n *   - Tripping on slow call ratio (too many long-running commands suggest\n *     a hung subprocess that the model doesn't know how to kill)\n *   - Rate-limiting bursts (rapid succession of commands without reading\n *     output suggests the model isn't processing results)\n *   - Auto-recovering after a cooldown period so a fixed model can resume\n *\n * The breaker is owned by the ProcessRegistry so any tool that registers\n * a process participates in the same circuit. \"Per-tool\" isolation is\n * intentionally NOT implemented — the model treats bash/exec as one\n * resource pool; isolating them would let the model route around the\n * breaker by alternating which tool it uses.\n */\n\nexport interface CircuitBreakerConfig {\n  /**\n   * Consecutive failures before trip. Default: 5.\n   * A single success resets this counter to 0.\n   */\n  maxConsecutiveFailures?: number | undefined;\n  /**\n   * Slow-call threshold in ms. A call that runs longer than this is\n   * counted as \"slow\". Default: 60_000 (1 minute).\n   */\n  slowCallThresholdMs?: number | undefined;\n  /**\n   * Max slow calls before trip (within the sliding window). Default: 3.\n   */\n  maxSlowCalls?: number | undefined;\n  /**\n   * Sliding window for rate-limit and slow-call counting, in ms.\n   * Default: 60_000 (1 minute).\n   */\n  windowMs?: number | undefined;\n  /**\n   * Max calls within the sliding window. Default: 30.\n   * Burst exceeding this trips the breaker immediately.\n   */\n  maxCallsPerWindow?: number | undefined;\n  /**\n   * Cooldown before auto-recovery attempt, in ms. Default: 30_000 (30s).\n   * After this the breaker enters \"half-open\" state and allows one call\n   * through to test whether the problem is resolved.\n   */\n  cooldownMs?: number | undefined;\n}\n\ninterface CallRecord {\n  at: number;\n  /** True if the call threw or returned an is_error result. */\n  failed: boolean;\n  /** True if elapsed time exceeded slowCallThresholdMs. */\n  slow: boolean;\n}\n\ntype BreakerState = 'closed' | 'open' | 'half-open';\n\nconst DEFAULT_MAX_CONSECUTIVE_FAILURES = 5;\nconst DEFAULT_SLOW_CALL_THRESHOLD_MS = 180_000;\n// 3 minutes — balanced against the 5-minute bash timeout. Commands\n// running <3min are normal; 3-5min are \"slow\" and count toward the\n// breaker. 3 consecutive slow calls trip the circuit.\nconst DEFAULT_MAX_SLOW_CALLS = 3;\nconst DEFAULT_WINDOW_MS = 60_000;\nconst DEFAULT_MAX_CALLS_PER_WINDOW = 30;\nconst DEFAULT_COOLDOWN_MS = 30_000;\n\nexport interface CircuitBreakerSnapshot {\n  state: 'closed' | 'open' | 'half-open';\n  consecutiveFailures: number;\n  slowCallsInWindow: number;\n  callsInWindow: number;\n  windowMs: number;\n  cooldownRemainingMs: number | null;\n  lastFailureAt: number | null;\n  lastSlowAt: number | null;\n}\n\nexport class CircuitBreaker {\n  private readonly maxConsecutiveFailures: number;\n  private readonly slowCallThresholdMs: number;\n  private readonly maxSlowCalls: number;\n  private readonly windowMs: number;\n  private readonly maxCallsPerWindow: number;\n  private readonly cooldownMs: number;\n\n  private state: BreakerState = 'closed';\n  private consecutiveFailures = 0;\n  private window: CallRecord[] = [];\n  private lastFailureAt: number | null = null;\n  private lastSlowAt: number | null = null;\n  /** Timestamp when the breaker was opened (for cooldown calculation). */\n  private openedAt: number | null = null;\n\n  /**\n   * Master enable flag. When false the breaker is bypassed: `beforeCall`\n   * always returns true and `afterCall` records nothing. The class itself\n   * defaults to enabled (so the standalone unit tests exercise tripping); the\n   * ProcessRegistry flips this off until the user opts in via `/settings`.\n   */\n  private enabled = true;\n\n  /**\n   * Fired (best-effort) when the breaker transitions into the `open` state.\n   * The registry uses this to arm its auto kill/reset countdown.\n   */\n  onTrip?: (() => void) | undefined;\n  /**\n   * Fired (best-effort) when the breaker returns to `closed` after having been\n   * open/half-open. The registry uses this to cancel a pending kill/reset.\n   */\n  onReset?: (() => void) | undefined;\n\n  constructor(config: CircuitBreakerConfig = {}) {\n    this.maxConsecutiveFailures = config.maxConsecutiveFailures ?? DEFAULT_MAX_CONSECUTIVE_FAILURES;\n    this.slowCallThresholdMs = config.slowCallThresholdMs ?? DEFAULT_SLOW_CALL_THRESHOLD_MS;\n    this.maxSlowCalls = config.maxSlowCalls ?? DEFAULT_MAX_SLOW_CALLS;\n    this.windowMs = config.windowMs ?? DEFAULT_WINDOW_MS;\n    this.maxCallsPerWindow = config.maxCallsPerWindow ?? DEFAULT_MAX_CALLS_PER_WINDOW;\n    this.cooldownMs = config.cooldownMs ?? DEFAULT_COOLDOWN_MS;\n  }\n\n  /** Toggle the master enable. Disabling resets to a clean `closed` state. */\n  setEnabled(enabled: boolean): void {\n    if (this.enabled === enabled) return;\n    this.enabled = enabled;\n    if (!enabled) this._reset();\n  }\n\n  get isEnabled(): boolean {\n    return this.enabled;\n  }\n\n  /**\n   * Returns true if the circuit allows a new call to proceed.\n   * When false, callers should abort the tool call and return a\n   * circuit-breaker error instead of spawning a process.\n   */\n  get canProceed(): boolean {\n    if (!this.enabled) return true;\n    this._checkStateTransition();\n    return this.state !== 'open';\n  }\n\n  /**\n   * Snapshot of the current breaker state for observability (`/kill`).\n   */\n  snapshot(): CircuitBreakerSnapshot {\n    this._checkStateTransition();\n    const now = Date.now();\n    let cooldownRemaining: number | null = null;\n    if (this.openedAt !== null && this.state === 'open') {\n      const elapsed = now - this.openedAt;\n      cooldownRemaining = Math.max(0, this.cooldownMs - elapsed);\n    }\n    return {\n      state: this.state,\n      consecutiveFailures: this.consecutiveFailures,\n      slowCallsInWindow: this.window.filter((c) => c.slow).length,\n      callsInWindow: this.window.length,\n      windowMs: this.windowMs,\n      cooldownRemainingMs: cooldownRemaining,\n      lastFailureAt: this.lastFailureAt,\n      lastSlowAt: this.lastSlowAt,\n    };\n  }\n\n  /**\n   * Call this BEFORE spawning a bash/exec process.\n   * Returns true if the call is allowed; false if the breaker is open.\n   * When false, callers MUST NOT spawn a process.\n   *\n   * @param bypass - If true, skip the circuit breaker check entirely.\n   *                  Use for background/fire-and-forget processes that should\n   *                  not affect breaker state.\n   */\n  beforeCall(bypass = false): boolean {\n    if (bypass || !this.enabled) return true;\n    this._checkStateTransition();\n    if (this.state === 'open') return false;\n    return true;\n  }\n\n  /**\n   * Call this AFTER a bash/exec process finishes (success or failure).\n   * `durationMs` is the wall-clock time the process ran.\n   * `failed` is true when the process returned a non-zero exit code or\n   * threw an exception before spawning.\n   *\n   * @param bypass - If true, do not update breaker state.\n   *                  Use for background/fire-and-forget processes.\n   */\n  afterCall(durationMs: number, failed: boolean, bypass = false): void {\n    if (bypass || !this.enabled) return;\n\n    const now = Date.now();\n\n    if (this.state === 'half-open') {\n      // First call through after cooldown — if it failed, go back to open.\n      if (failed) {\n        this._trip();\n        return;\n      }\n      // Success in half-open → reset to closed.\n      this._reset();\n      return;\n    }\n\n    // Prune old records outside the sliding window.\n    this._pruneWindow(now);\n\n    const slow = durationMs >= this.slowCallThresholdMs;\n    this.window.push({ at: now, failed, slow });\n\n    if (failed) {\n      this.consecutiveFailures++;\n      this.lastFailureAt = now;\n      if (this.consecutiveFailures >= this.maxConsecutiveFailures) {\n        this._trip();\n      }\n      return;\n    }\n\n    // Success: reset consecutive failure counter.\n    this.consecutiveFailures = 0;\n\n    if (slow) {\n      this.lastSlowAt = now;\n      const slowCount = this.window.filter((c) => c.slow).length;\n      if (slowCount >= this.maxSlowCalls) {\n        this._trip();\n      }\n    }\n\n    const callCount = this.window.length;\n    if (callCount >= this.maxCallsPerWindow) {\n      // Rate limit exceeded. This is a soft trip — we reset the window\n      // and let the next call try immediately (the caller will still see\n      // canProceed=false until the window drains naturally).\n      this._trip();\n    }\n  }\n\n  /** Force the breaker open. Used by /kill force and Ctrl+C. */\n  forceOpen(): void {\n    this._trip();\n  }\n\n  /** Force a reset to closed. Used by tests and /kill reset. */\n  forceReset(): void {\n    this._reset();\n  }\n\n  private _trip(): void {\n    if (this.state === 'open') return; // already open\n    this.state = 'open';\n    this.openedAt = Date.now();\n    // P3 #23 (before-release.md): clear the window on trip. Old records are\n    // irrelevant once tripped — the breaker starts fresh after cooldown\n    // (half-open → closed resets the counters). Without this the window array\n    // holds onto CallRecord entries for its lifetime if no new afterCall()\n    // arrives (which is the case when the breaker stays open and no new calls\n    // are attempted).\n    this.window = [];\n    // Best-effort: never let a listener failure corrupt breaker state.\n    try {\n      this.onTrip?.();\n    } catch {\n      /* ignored — observability hook only */\n    }\n  }\n\n  private _reset(): void {\n    const wasRecovering = this.state !== 'closed';\n    this.state = 'closed';\n    this.consecutiveFailures = 0;\n    this.window = [];\n    this.openedAt = null;\n    // Only notify on a real recovery (open/half-open → closed), not on the\n    // initial closed state or an idempotent re-reset.\n    if (wasRecovering) {\n      try {\n        this.onReset?.();\n      } catch {\n        /* ignored — observability hook only */\n      }\n    }\n  }\n\n  /** Transition from open → half-open when cooldown elapses. */\n  private _checkStateTransition(): void {\n    if (this.state !== 'open' || this.openedAt === null) return;\n    const elapsed = Date.now() - this.openedAt;\n    if (elapsed >= this.cooldownMs) {\n      this.state = 'half-open';\n      this.openedAt = null;\n    }\n  }\n\n  private _pruneWindow(now: number): void {\n    const cutoff = now - this.windowMs;\n    this.window = this.window.filter((c) => c.at >= cutoff);\n  }\n}"]}

package/dist/codebase-index/index.js

@@ -405,6 +405,8 @@ var IndexStore = class {
     this.db.exec("CREATE INDEX IF NOT EXISTS idx_s_kind ON symbols(kind)");
     this.db.exec("CREATE INDEX IF NOT EXISTS idx_s_lang ON symbols(lang)");
     this.db.exec("CREATE INDEX IF NOT EXISTS idx_s_file ON symbols(file)");
+    this.db.exec("CREATE INDEX IF NOT EXISTS idx_s_lang_kind ON symbols(lang, kind)");
+    this.db.exec("CREATE INDEX IF NOT EXISTS idx_s_file_fk ON symbols(file_fk)");
     this.db.exec(`
       CREATE TABLE IF NOT EXISTS refs (
         id INTEGER PRIMARY KEY,
@@ -1317,9 +1319,9 @@ async function syncGoParse(filePath, content, lang) {
   }
 }
 async function parseSymbols3(opts) {
-  const { file, lang } = opts;
+  const { file, content, lang } = opts;
   try {
-    return await syncPyParse(file, lang);
+    return await syncPyParse(file, content, lang);
   } catch {
     return { file, lang, symbols: [], mtimeMs: Date.now() };
   }
@@ -1387,8 +1389,7 @@ syms = []
 errors = []
 
 try:
-    with open(sys.argv[1], "r", encoding="utf-8") as f:
-        source = f.read()
+    source = sys.stdin.read()
     tree = ast.parse(source, filename=sys.argv[1])
 except Exception as e:
     errors.append(str(e))
@@ -1528,16 +1529,21 @@ visitor.visit(tree)
 
 print(json.dumps([s.to_dict() for s in syms]))
 `;
-async function syncPyParse(filePath, lang) {
+var _cachedScriptPath = null;
+async function syncPyParse(filePath, content, lang) {
   try {
-    const tmpDir = path4.join(os.tmpdir(), "ws-py-parse");
-    await fs6.mkdir(tmpDir, { recursive: true });
-    const scriptPath = path4.join(tmpDir, "parse.py");
-    await fs6.writeFile(scriptPath, PY_PARSE_SCRIPT, "utf8");
-    const proc = spawn("python", [scriptPath, filePath], {
+    if (!_cachedScriptPath) {
+      const tmpDir = path4.join(os.tmpdir(), "ws-py-parse");
+      await fs6.mkdir(tmpDir, { recursive: true });
+      _cachedScriptPath = path4.join(tmpDir, "parse.py");
+      await fs6.writeFile(_cachedScriptPath, PY_PARSE_SCRIPT, "utf8");
+    }
+    const proc = spawn("python", [_cachedScriptPath, filePath], {
       stdio: ["pipe", "pipe", "pipe"],
       windowsHide: true
     });
+    proc.stdin?.write(content);
+    proc.stdin?.end();
     let stdout = "";
     proc.stdout?.on("data", (chunk) => {
       stdout += chunk.toString();
@@ -2204,7 +2210,7 @@ async function parseFile(file, content, lang) {
     case "go":
       return parseSymbols2({ file, content, lang: "go" });
     case "py":
-      return parseSymbols3({ file, lang: "py" });
+      return parseSymbols3({ file, content, lang: "py" });
     case "rs":
       return parseSymbols4({ file, content, lang: "rs" });
     case "json":
@@ -2235,10 +2241,12 @@ async function runIndexerWithStore(store, opts) {
   let symbolsIndexed = 0;
   const isGitIgnored = await loadGitignoreMatcher(projectRoot);
   let files;
+  let discoveredFiles = null;
   if (opts.files && opts.files.length > 0) {
     files = opts.files.map((f) => path4.resolve(projectRoot, f)).filter((f) => !isGitIgnored(path4.relative(projectRoot, f).replace(/\\/g, "/"), false));
   } else {
     files = await findSourceFiles(projectRoot, ignore, isGitIgnored, signal);
+    discoveredFiles = new Set(files);
   }
   if (langs && langs.length > 0) {
     const langSet = new Set(langs);
@@ -2356,11 +2364,11 @@ async function runIndexerWithStore(store, opts) {
       filesIndexed++;
     }
   }
-  for (const [file_] of existingMeta) {
-    try {
-      await fs6.stat(file_);
-    } catch {
-      store.deleteFile(file_);
+  if (discoveredFiles) {
+    for (const [file_] of existingMeta) {
+      if (!discoveredFiles.has(file_)) {
+        store.deleteFile(file_);
+      }
     }
   }
   const durationMs = Date.now() - startMs;