loki-mode 8.55.0 → 8.63.0

package/SKILL.md

@@ -3,7 +3,7 @@ name: loki-mode
 description: Autonomous spec-driven build system with a built-in trust layer. It does not call work done until it is verified (RARV-C closure loop, 8 quality gates, completion council, verified-completion evidence gate). Triggers on "Loki Mode". Takes a spec (PRD, GitHub issue, OpenAPI doc, etc.) to deployed product with minimal human intervention. Provider-agnostic. Requires --dangerously-skip-permissions flag.
 ---
 
-# Loki Mode v8.55.0
+# Loki Mode v8.63.0
 
 **You are an autonomous agent. You make decisions. You do not ask questions. You do not stop.**
 
@@ -469,4 +469,4 @@ See `CHANGELOG.md` entries [7.5.7], [7.5.8], [7.5.13] for the per-fix list and r
 
 ---
 
-**v8.55.0 | [Autonomi](https://www.autonomi.dev/) flagship product | ~410 lines core**
+**v8.63.0 | [Autonomi](https://www.autonomi.dev/) flagship product | ~410 lines core**

package/VERSION

@@ -1 +1 @@
-8.55.0
+8.63.0

package/autonomy/run.sh

@@ -21379,7 +21379,23 @@ except Exception:
         # shellcheck disable=SC1090
         . "${SCRIPT_DIR}/spec-interrogation.sh" 2>/dev/null || true
         if type spec_interrogation_run &>/dev/null; then
+            # TIMED. Startup was completely unmeasured: on a real run, 128
+            # SECONDS elapsed between session_start and iteration_start -- over
+            # two minutes in which the user sees nothing and no agent work has
+            # begun. Nothing in .loki/events.jsonl accounted for any of it, so
+            # the interval could not be attributed, let alone optimised.
+            #
+            # This step calls the provider, so it is the prime suspect for the
+            # bulk of that window. Naming it turns "startup is slow" into a
+            # number, the same way stage timings turned "the run is slow" into
+            # "the agent call is 93% of wall clock".
+            #
+            # Uses the existing emit_stage_complete channel, so measure-run.sh
+            # and every other consumer pick it up with no new plumbing.
+            local _si_t0
+            _si_t0=$(date +%s 2>/dev/null || echo 0)
             spec_interrogation_run "$prd_path" || true
+            emit_stage_complete "spec_interrogation" "pass" "$_si_t0" 2>/dev/null || true
         fi
         # #87: no-HITL fast-fail on an unresolved spec-INTERNAL contradiction.
         # A contradiction (class=contradictory) is NEVER auto-acked (P2-4) and only
@@ -22301,6 +22317,11 @@ def process_stream():
     # message. Stays False when partial messages are off (no stream_event lines).
     streamed_text_blocks = False
 
+    # Per-turn usage samples for the context-growth record (L1). Appended on
+    # every assistant message; written once at the result event. Bounded below
+    # so a pathological run cannot grow this without limit.
+    _turn_usage = []
+
     for line in sys.stdin:
         line = line.strip()
         if not line:
@@ -22336,6 +22357,43 @@ def process_stream():
                 # Extract and print assistant text
                 message = data.get("message", {})
                 content = message.get("content", [])
+
+                # PER-TURN CONTEXT GROWTH (read-only instrumentation, L1).
+                #
+                # WHY. One measured iteration re-sent 10,651,759 cached-read
+                # tokens to produce 34,729 output tokens -- a 307:1 ratio, in a
+                # SINGLE provider call (one iteration_start, one
+                # result-cost-1.json, so cross-iteration reuse is ruled out).
+                # That call was 100% of measured stage time.
+                #
+                # The provider cache already saved us 10x ($31.96 -> $3.20 of a
+                # $4.74 iteration). We are not missing a cache; the ORDER being
+                # discounted is enormous, and cached reads are still 67% of the
+                # bill. Those tokens are prefill the model must process serially
+                # before emitting a character, so this is the only measured lever
+                # that touches BOTH cost and the 744s.
+                #
+                # "the tool loop re-accumulates history" is INFERRED from the
+                # ratio, not observed. Trimming context on an inference is how
+                # you ship an agent that forgets what it already tried and redoes
+                # the work -- raising iterations and costing more than it saves.
+                # So this MEASURES per turn and trims nothing. The cut is a
+                # separate decision, gated on iterations-to-done rather than on
+                # a token count.
+                try:
+                    _tu = (message.get("usage") or {})
+                    _tcr = _tu.get("cache_read_input_tokens")
+                    if isinstance(_tcr, int) and _tcr >= 0:
+                        _turn_usage.append({
+                            "turn": len(_turn_usage) + 1,
+                            "cache_read_tokens": _tcr,
+                            "input_tokens": _tu.get("input_tokens", 0) or 0,
+                            "output_tokens": _tu.get("output_tokens", 0) or 0,
+                            "cache_creation_tokens":
+                                _tu.get("cache_creation_input_tokens", 0) or 0,
+                        })
+                except Exception:
+                    pass
                 for item in content:
                     if item.get("type") == "text":
                         text = item.get("text", "")
@@ -22488,6 +22546,44 @@ def process_stream():
                         "cache_read_tokens": _u.get("cache_read_input_tokens", 0),
                         "cache_creation_tokens": _u.get("cache_creation_input_tokens", 0),
                     }
+                    # CONTEXT-GROWTH RECORD (L1). Written whenever turns were
+                    # observed, independently of whether cost was reported --
+                    # the growth shape is the finding, and tying it to
+                    # total_cost_usd would lose it on every provider that does
+                    # not report dollars (codex reports tokens, never cost).
+                    if _turn_usage:
+                        try:
+                            os.makedirs(".loki/metrics", exist_ok=True)
+                            _first = _turn_usage[0]["cache_read_tokens"]
+                            _last = _turn_usage[-1]["cache_read_tokens"]
+                            _growth = {
+                                "iteration": _iter,
+                                "turns": len(_turn_usage),
+                                "first_turn_cache_read": _first,
+                                "last_turn_cache_read": _last,
+                                # The headline: how much bigger the context got
+                                # between the first and last turn of ONE call.
+                                "growth_factor": (round(_last / _first, 2)
+                                                  if _first > 0 else None),
+                                "total_cache_read": sum(
+                                    t["cache_read_tokens"] for t in _turn_usage),
+                                "total_output": sum(
+                                    t["output_tokens"] for t in _turn_usage),
+                                # Bounded sample: the shape is visible in the
+                                # first and last few turns, and an unbounded
+                                # array would make this file grow with the run.
+                                "sample": (_turn_usage[:5] + _turn_usage[-5:]
+                                           if len(_turn_usage) > 10
+                                           else _turn_usage),
+                            }
+                            _gp = ".loki/metrics/context-growth-" + str(_iter) + ".json"
+                            _gt = _gp + ".tmp"
+                            with open(_gt, "w") as _gf:
+                                json.dump(_growth, _gf)
+                            os.replace(_gt, _gp)
+                        except Exception:
+                            pass
+
                     if _rec["total_cost_usd"] is not None:
                         os.makedirs(".loki/metrics", exist_ok=True)
                         _p = ".loki/metrics/result-cost-" + str(_iter) + ".json"
@@ -22635,6 +22731,33 @@ if __name__ == "__main__":
         # costs zero extra subprocesses -- we pass the existing epoch through.
         emit_stage_complete "agent" "$([ "$exit_code" -eq 0 ] 2>/dev/null && echo pass || echo fail)" "$start_time"
 
+        # AGENT PROMPT SIZE. The call this brackets is 93% of a run's wall clock
+        # (1814s of 1941s measured), and its INPUT was never measured -- every
+        # reviewer logs its prompt bytes, the dominant call logged nothing.
+        #
+        # Prompt size is the input side of that 93% and one of the few levers we
+        # actually control: we cannot make the provider faster, but we can send
+        # it less. Without the number, "the prompt got bigger" is invisible
+        # until it shows up as latency and cost with no attributable cause --
+        # the same gap W1 closed for tokens.
+        #
+        # Costs one `wc -c` on a string already in memory: no subprocess for the
+        # provider, no extra file read. Emitted on the existing event channel so
+        # measure-run.sh and the receipt pick it up with no new plumbing.
+        if [ -n "${prompt:-}" ]; then
+            local _agent_prompt_bytes
+            _agent_prompt_bytes=$(printf '%s' "$prompt" | wc -c 2>/dev/null | tr -d ' ')
+            case "$_agent_prompt_bytes" in
+                ''|*[!0-9]*) ;;   # unmeasurable -> emit nothing, never a zero
+                *)
+                    emit_event_json "agent_prompt" \
+                        "bytes=$_agent_prompt_bytes" \
+                        "iteration=${ITERATION_COUNT:-0}" \
+                        "duration_s=$duration" 2>/dev/null || true
+                    ;;
+            esac
+        fi
+
         # TIME TO FIRST ARTIFACT. The companion to seconds_to_first_preview, for
         # the case that has no preview at all.
         #
@@ -22959,6 +23082,14 @@ if __name__ == "__main__":
                     local tc_count
                     tc_count=$(track_gate_failure "test_coverage")
                     gate_failures="${gate_failures}test_coverage,"
+                    # Fourth dead branch, found by deriving the handled-gate set
+                    # from the writer instead of hardcoding it: test_coverage
+                    # maps to quality/test-results.json and had no caller either.
+                    if [ "$(gate_failure_disposition "$tc_count")" != "block" ]; then
+                        local _tc_thresh="$GATE_CLEAR_LIMIT"
+                        [ "$GATE_ESCALATE_LIMIT" -lt "$_tc_thresh" ] && _tc_thresh="$GATE_ESCALATE_LIMIT"
+                        write_gate_escalation_guidance "test_coverage" "$tc_count" "$_tc_thresh" || true
+                    fi
                     # P0-1 Fix A: distinguish a coverage-only block (tests passed,
                     # enforced coverage below threshold) from a genuine tests-red
                     # block in the log so the operator is not misled.
@@ -22994,6 +23125,23 @@ if __name__ == "__main__":
                         mk_count=$(track_gate_failure "mock_integrity")
                         gate_failures="${gate_failures}mock_integrity,"
                         log_warn "Mock integrity gate FAILED ($mk_count consecutive) - CRITICAL/HIGH mock problems"
+                        # Escalation guidance was DEAD for this gate.
+                        # write_gate_escalation_guidance already handles
+                        # mock_integrity, mutation_integrity and test_coverage by
+                        # name -- and only code_review ever called it, so those
+                        # branches could never run.
+                        #
+                        # Measured: on a real run mock_integrity failed THREE
+                        # times (the most of any gate) and
+                        # .loki/signals/GATE_ESCALATION.json was never written.
+                        # The agent was told the gate failed and never handed the
+                        # findings file that says WHY, which is the 56%
+                        # "did not attempt to recover" failure shape.
+                        if [ "$(gate_failure_disposition "$mk_count")" != "block" ]; then
+                            local _mk_thresh="$GATE_CLEAR_LIMIT"
+                            [ "$GATE_ESCALATE_LIMIT" -lt "$_mk_thresh" ] && _mk_thresh="$GATE_ESCALATE_LIMIT"
+                            write_gate_escalation_guidance "mock_integrity" "$mk_count" "$_mk_thresh" || true
+                        fi
                         # F0, third gate. Measured on the v8.49.0 FireLater run:
                         # mock_integrity failed 3 times -- MORE than any other
                         # gate -- and was not wired to the stuck check, so an
@@ -23030,6 +23178,15 @@ if __name__ == "__main__":
                     mt_count=$(track_gate_failure "mutation_integrity")
                     gate_failures="${gate_failures}mutation_integrity,"
                     log_warn "Mutation integrity gate FAILED ($mt_count consecutive) - HIGH test-fitting detected"
+                    # Same dead-branch fix as mock_integrity above:
+                    # write_gate_escalation_guidance maps mutation_integrity to
+                    # mutation-findings.txt and nothing ever called it with that
+                    # gate name, so the mapping could never fire.
+                    if [ "$(gate_failure_disposition "$mt_count")" != "block" ]; then
+                        local _mt_thresh="$GATE_CLEAR_LIMIT"
+                        [ "$GATE_ESCALATE_LIMIT" -lt "$_mt_thresh" ] && _mt_thresh="$GATE_ESCALATE_LIMIT"
+                        write_gate_escalation_guidance "mutation_integrity" "$mt_count" "$_mt_thresh" || true
+                    fi
                     # F0: an unchanging cause means the next iteration reaches
                     # the same verdict. FireLater burned 3 iterations here on a
                     # detector that was never packaged, failing in 0-1s each

package/dashboard/__init__.py

@@ -7,7 +7,7 @@ Modules:
     control: Session control API (start/stop/pause/resume)
 """
 
-__version__ = "8.55.0"
+__version__ = "8.63.0"
 
 # Expose the control app for easy import
 try:

package/dashboard/server.py

@@ -559,6 +559,40 @@ start_time = datetime.now(timezone.utc)
 _dashboard_start_time = time.time()
 
 
+def _registry_run_alive(loki_dir: _Path) -> bool:
+    """True when .loki/pids/ holds a LIVE wrapper/runner process.
+
+    Third liveness source for a CLI-started background run, which writes
+    neither loki.pid nor session.json (run.sh only UPDATES session.json when it
+    already exists). Both of those checks therefore fail for `loki start` and
+    the run falls through to "stopped" while it is actively building.
+
+    The kind filter is load-bearing: .loki/pids/ also registers the dashboard
+    itself, the status-monitor and the resource-monitor, none of which carry a
+    "kind" key. Accepting any live pid here would let the dashboard's own
+    process prove the run is alive, turning a false-stopped into a permanent
+    false-running. Keep it to wrapper/runner.
+
+    Liveness is proven with os.kill(pid, 0), never by the file's presence -- a
+    stale entry from a crashed run must NOT read as alive.
+    """
+    try:
+        for _entry in (loki_dir / "pids").glob("*.json"):
+            _rec = _safe_json_read(_entry, {})
+            if not isinstance(_rec, dict):
+                continue
+            if _rec.get("kind") not in ("wrapper", "runner"):
+                continue
+            try:
+                os.kill(int(_rec.get("pid", 0)), 0)
+            except (ValueError, TypeError, OSError, ProcessLookupError):
+                continue
+            return True
+    except OSError:
+        pass
+    return False
+
+
 async def _push_loki_state_loop() -> None:
     """Background loop: push .loki/ state changes to all WebSocket clients.
 
@@ -679,35 +713,15 @@ async def _push_loki_state_loop() -> None:
                                 pass
 
                         # Third source: the .loki/pids/ registry, which a
-                        # CLI-started background run DOES write. Without this
-                        # the dashboard reported STOPPED for a healthy build:
-                        # `loki start` writes neither loki.pid nor session.json
-                        # (run.sh only UPDATES session.json when it already
-                        # exists), so both checks above failed and every such
-                        # run fell through to "stopped" while it was actively
-                        # working. Confirmed against a live build: STATUS.txt
-                        # said BUILDING and iterations were advancing while the
-                        # dashboard showed STOPPED with 0 agents.
-                        #
-                        # Liveness is proven with os.kill(pid, 0), never by the
-                        # file's presence -- a stale entry from a crashed run
-                        # must NOT read as alive, which is the same
-                        # anti-stale rule BUG-NEW-006 established above.
+                        # CLI-started background run DOES write. Shared with
+                        # /api/status via _registry_run_alive so both live
+                        # surfaces agree -- they previously did not: on a real
+                        # `loki start` build this stream broadcast "running"
+                        # while /api/status returned "stopped" for the SAME run
+                        # in the same second, because only this copy had the
+                        # pids/ source.
                         if not _pid_alive:
-                            try:
-                                _pid_dir = loki_dir / "pids"
-                                for _entry in _pid_dir.glob("*.json"):
-                                    _rec = _safe_json_read(_entry, {})
-                                    if _rec.get("kind") not in ("wrapper", "runner"):
-                                        continue
-                                    try:
-                                        os.kill(int(_rec.get("pid", 0)), 0)
-                                    except (ValueError, OSError, ProcessLookupError):
-                                        continue
-                                    _pid_alive = True
-                                    break
-                            except OSError:
-                                pass
+                            _pid_alive = _registry_run_alive(loki_dir)
 
                         status_str = raw.get("mode", "autonomous")
                         # Control files are the AUTHORITY, and they are checked
@@ -1438,6 +1452,13 @@ async def get_status() -> StatusResponse:
         if not mode:
             mode = "autonomous"
 
+    # Third source: .loki/pids/ registry (see _registry_run_alive). A
+    # CLI-started background run writes neither loki.pid nor session.json, so
+    # both checks above miss it and a healthy build reported "stopped" here
+    # while the WS stream -- which already had this source -- said "running".
+    if not running:
+        running = _registry_run_alive(loki_dir)
+
     # Determine status string
     if not running:
         status = "stopped"

package/loki-ts/dist/loki.js

@@ -1,5 +1,5 @@
 // @bun
-var h_=Object.create;var{getPrototypeOf:v_,defineProperty:rK,getOwnPropertyNames:g_}=Object;var m_=Object.prototype.hasOwnProperty;function u_(Z){return this[Z]}var p_,d_,c_=(Z,X,Q)=>{var Y=Z!=null&&typeof Z==="object";if(Y){var J=X?p_??=new WeakMap:d_??=new WeakMap,z=J.get(Z);if(z)return z}Q=Z!=null?h_(v_(Z)):{};let K=X||!Z||!Z.__esModule?rK(Q,"default",{value:Z,enumerable:!0}):Q;for(let $ of g_(Z))if(!m_.call(K,$))rK(K,$,{get:u_.bind(Z,$),enumerable:!0});if(Y)J.set(Z,K);return K};var qQ=(Z,X)=>()=>(X||Z((X={exports:{}}).exports,X),X.exports);var l_=(Z)=>Z;function i_(Z,X){this[Z]=l_.bind(null,X)}var l0=(Z,X)=>{for(var Q in X)rK(Z,Q,{get:X[Q],enumerable:!0,configurable:!0,set:i_.bind(X,Q)})};var p=(Z,X)=>()=>(Z&&(X=Z(Z=0)),X);var e0=import.meta.require;var kO={};l0(kO,{lokiDir:()=>j0,homeLokiDir:()=>P4,findRepoRootForVersion:()=>eK,REPO_ROOT:()=>r0});import{resolve as n7,dirname as tK}from"path";import{fileURLToPath as a_}from"url";import{existsSync as GQ}from"fs";import{homedir as s_}from"os";function n_(){let Z=RO;for(let X=0;X<6;X++){if(GQ(n7(Z,"VERSION"))&&GQ(n7(Z,"autonomy/run.sh")))return Z;let Q=tK(Z);if(Q===Z)break;Z=Q}return n7(RO,"..","..","..")}function eK(Z){let X=Z;for(let Q=0;Q<6;Q++){if(GQ(n7(X,"VERSION"))&&GQ(n7(X,"autonomy/run.sh")))return X;let Y=tK(X);if(Y===X)break;X=Y}return n7(Z,"..","..","..")}function j0(){return process.env.LOKI_DIR??n7(process.cwd(),".loki")}function P4(){return n7(s_(),".loki")}var RO,r0;var G8=p(()=>{RO=tK(a_(import.meta.url));r0=n_()});import{readFileSync as o_}from"fs";import{resolve as r_,dirname as t_}from"path";import{fileURLToPath as e_}from"url";function f3(){if(h5!==null)return h5;let Z="8.55.0";if(typeof Z==="string"&&Z.length>0)return h5=Z,h5;try{let X=t_(e_(import.meta.url)),Q=eK(X);h5=o_(r_(Q,"VERSION"),"utf-8").trim()}catch{h5="unknown"}return h5}var h5=null;var HQ=p(()=>{G8()});var 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+var h_=Object.create;var{getPrototypeOf:v_,defineProperty:rK,getOwnPropertyNames:g_}=Object;var m_=Object.prototype.hasOwnProperty;function u_(Z){return this[Z]}var p_,d_,c_=(Z,X,Q)=>{var Y=Z!=null&&typeof Z==="object";if(Y){var J=X?p_??=new WeakMap:d_??=new WeakMap,z=J.get(Z);if(z)return z}Q=Z!=null?h_(v_(Z)):{};let K=X||!Z||!Z.__esModule?rK(Q,"default",{value:Z,enumerable:!0}):Q;for(let $ of g_(Z))if(!m_.call(K,$))rK(K,$,{get:u_.bind(Z,$),enumerable:!0});if(Y)J.set(Z,K);return K};var qQ=(Z,X)=>()=>(X||Z((X={exports:{}}).exports,X),X.exports);var l_=(Z)=>Z;function i_(Z,X){this[Z]=l_.bind(null,X)}var l0=(Z,X)=>{for(var Q in X)rK(Z,Q,{get:X[Q],enumerable:!0,configurable:!0,set:i_.bind(X,Q)})};var p=(Z,X)=>()=>(Z&&(X=Z(Z=0)),X);var e0=import.meta.require;var kO={};l0(kO,{lokiDir:()=>j0,homeLokiDir:()=>P4,findRepoRootForVersion:()=>eK,REPO_ROOT:()=>r0});import{resolve as n7,dirname as tK}from"path";import{fileURLToPath as a_}from"url";import{existsSync as GQ}from"fs";import{homedir as s_}from"os";function n_(){let Z=RO;for(let X=0;X<6;X++){if(GQ(n7(Z,"VERSION"))&&GQ(n7(Z,"autonomy/run.sh")))return Z;let Q=tK(Z);if(Q===Z)break;Z=Q}return n7(RO,"..","..","..")}function eK(Z){let X=Z;for(let Q=0;Q<6;Q++){if(GQ(n7(X,"VERSION"))&&GQ(n7(X,"autonomy/run.sh")))return X;let Y=tK(X);if(Y===X)break;X=Y}return n7(Z,"..","..","..")}function j0(){return process.env.LOKI_DIR??n7(process.cwd(),".loki")}function P4(){return n7(s_(),".loki")}var RO,r0;var G8=p(()=>{RO=tK(a_(import.meta.url));r0=n_()});import{readFileSync as o_}from"fs";import{resolve as r_,dirname as t_}from"path";import{fileURLToPath as e_}from"url";function f3(){if(h5!==null)return h5;let Z="8.63.0";if(typeof Z==="string"&&Z.length>0)return h5=Z,h5;try{let X=t_(e_(import.meta.url)),Q=eK(X);h5=o_(r_(Q,"VERSION"),"utf-8").trim()}catch{h5="unknown"}return h5}var h5=null;var HQ=p(()=>{G8()});var 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 `),process.stdout.write(`Install with:
 `),process.stdout.write(`  brew install jq    (macOS)
 `),process.stdout.write(`  apt install jq     (Debian/Ubuntu)
@@ -1227,4 +1227,4 @@ Set LOKI_LEGACY_BASH=1 to force the bash CLI for every command.
 `),2}case"start":{let{runStart:Y}=await Promise.resolve().then(() => (b_(),y_));return Y(Q)}default:return process.stderr.write(`Unknown command: ${X}
 `),process.stderr.write(__),2}}cO();process.on("SIGINT",()=>process.exit(130));process.on("SIGTERM",()=>process.exit(143));var fW0=await _W0(Bun.argv.slice(2));process.exit(fW0);
 
-//# debugId=16FDE245B508551364756E2164756E21
+//# debugId=389F590913B3AC8264756E2164756E21

package/mcp/__init__.py

@@ -75,4 +75,4 @@ try:
 except ImportError:
     __all__ = ['mcp']
 
-__version__ = '8.55.0'
+__version__ = '8.63.0'

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "loki-mode",
   "mcpName": "io.github.asklokesh/loki-mode",
-  "version": "8.55.0",
+  "version": "8.63.0",
   "description": "Loki Mode by Autonomi. Autonomous spec-to-product system: takes a PRD, GitHub issue, OpenAPI/JSON/YAML, or one-line brief to a deployed app via the RARV-C closure loop with 8 quality gates. Provider-agnostic (Claude Code, OpenAI Codex, Cline, Aider).",
   "keywords": [
     "agent",

package/plugins/loki-mode/.claude-plugin/plugin.json

@@ -2,7 +2,7 @@
   "$schema": "https://json.schemastore.org/claude-code-plugin-manifest.json",
   "name": "loki-mode",
   "displayName": "Loki Mode",
-  "version": "8.55.0",
+  "version": "8.63.0",
   "description": "Autonomous spec-to-product build system with a built-in trust layer (RARV-C closure loop, 8 quality gates, completion council). Ships Loki's spec-hardening, drift-detection, and deterministic PR verification commands plus the Loki MCP server.",
   "author": {
     "name": "Autonomi",

package/tools/index-codebase.py

@@ -320,6 +320,19 @@ def chunk_markdown_file(filepath: Path) -> list[dict]:
     return chunks
 
 
+def _is_skipped(p: Path) -> bool:
+    """True when a path lies inside a skipped directory.
+
+    Compares components of the path RELATIVE to PROJECT_ROOT. An absolute-path
+    substring test makes indexing depend on where the repo happens to live.
+    """
+    try:
+        rel = p.resolve().relative_to(PROJECT_ROOT)
+    except ValueError:
+        return False
+    return any(part in SKIP_DIRS for part in rel.parts)
+
+
 def collect_files() -> list[tuple[Path, str]]:
     """Collect all files to index with their type."""
     files = []
@@ -335,7 +348,12 @@ def collect_files() -> list[tuple[Path, str]]:
         for p in sorted(PROJECT_ROOT.glob(glob_pattern)):
             if p.name.startswith("__"):
                 continue
-            if any(skip in str(p) for skip in SKIP_DIRS):
+            # Match path COMPONENTS relative to the project root, never a
+            # substring of the absolute path. `.claude` in SKIP_DIRS plus a
+            # checkout living under .../.claude/worktrees/<name>/ meant EVERY
+            # python file matched and the index came back empty -- silently, as
+            # a search that returns nothing rather than an error.
+            if _is_skipped(p):
                 continue
             files.append((p, "python"))