loki-mode 7.98.0 → 7.99.1

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 v7.98.0
+# Loki Mode v7.99.1
 
 **You are an autonomous agent. You make decisions. You do not ask questions. You do not stop.**
 
@@ -408,4 +408,4 @@ See `CHANGELOG.md` entries [7.5.7], [7.5.8], [7.5.13] for the per-fix list and r
 
 ---
 
-**v7.98.0 | [Autonomi](https://www.autonomi.dev/) flagship product | ~260 lines core**
+**v7.99.1 | [Autonomi](https://www.autonomi.dev/) flagship product | ~260 lines core**

package/VERSION

@@ -1 +1 @@
-7.98.0
+7.99.1

package/autonomy/checklist-verify.py

@@ -97,8 +97,30 @@ def run_check(check: dict, project_dir: str, timeout: int) -> dict:
                         text=True,
                         timeout=timeout,
                     )
-                    result["passed"] = proc.returncode == 0
-                    result["output"] = (proc.stdout + proc.stderr)[:500]
+                    combined = proc.stdout + proc.stderr
+                    # Trust gate: a tests_pass check REQUIRES that at least one
+                    # test was actually discovered and run. jest is invoked with
+                    # --passWithNoTests, so a zero-match pattern exits 0 ("No
+                    # tests found ...") -- that would be a fake-green (a required
+                    # verification passing with nothing run). pytest exits 5 when
+                    # it collects no tests. Detect either no-test signal and fail
+                    # the check rather than report success on an empty run.
+                    no_tests = (
+                        "No tests found" in combined
+                        or "no tests ran" in combined.lower()
+                        or "no tests to run" in combined.lower()
+                        or proc.returncode == 5  # pytest: no tests collected
+                    )
+                    if no_tests:
+                        result["passed"] = False
+                        result["output"] = (
+                            "No tests discovered for required check "
+                            f"(pattern={pattern!r}); a tests_pass check must run "
+                            "at least one test. Output: "
+                        ) + combined[:400]
+                    else:
+                        result["passed"] = proc.returncode == 0
+                        result["output"] = combined[:500]
                 except subprocess.TimeoutExpired:
                     result["passed"] = None  # timeout = pending
                     result["output"] = f"Timed out after {timeout}s"

package/autonomy/run.sh

@@ -947,8 +947,24 @@ PYCHECK
         fi
         # (d) Defense-in-depth: reclaim the dashboard port only in the CLEAR
         # case, so we never kill a shared dashboard another project owns.
+        # BUT never kill a HEALTHY dashboard already serving on the port: that is
+        # almost always the user's own live dashboard (open in their browser), and
+        # killing it mid-use drops their session (ERR_CONNECTION_REFUSED, WS fail).
+        # A healthy server is reusable by every project, so probe /api/status first
+        # and only reclaim the port when nothing is answering (a genuinely stale
+        # listener). Opt out of the probe with LOKI_DASHBOARD_FORCE_RECLAIM=1.
         if command -v lsof >/dev/null 2>&1; then
-            lsof -ti:"${DASHBOARD_PORT:-57374}" -sTCP:LISTEN 2>/dev/null | xargs kill 2>/dev/null || true
+            local _dash_port="${DASHBOARD_PORT:-57374}"
+            local _dash_alive=""
+            if [ "${LOKI_DASHBOARD_FORCE_RECLAIM:-}" != "1" ] && command -v curl >/dev/null 2>&1; then
+                _dash_alive=$(curl -s -o /dev/null -w '%{http_code}' --max-time 1 \
+                    "http://127.0.0.1:${_dash_port}/api/status" 2>/dev/null || true)
+            fi
+            if [ "$_dash_alive" = "200" ]; then
+                log_info "Reusing the healthy dashboard already serving on port ${_dash_port} (not reclaiming)."
+            else
+                lsof -ti:"${_dash_port}" -sTCP:LISTEN 2>/dev/null | xargs kill 2>/dev/null || true
+            fi
         fi
     fi
 }
@@ -11230,6 +11246,7 @@ start_dashboard() {
     local original_port=$DASHBOARD_PORT
     local max_attempts=10
     local attempt=0
+    local DASHBOARD_REUSED=0
 
     while lsof -i :$DASHBOARD_PORT &>/dev/null && [ $attempt -lt $max_attempts ]; do
         # Check if it's our own dashboard
@@ -11238,7 +11255,24 @@ start_dashboard() {
             # Only kill if it's a Python/uvicorn dashboard process
             local proc_cmd=$(ps -p "$existing_pid" -o comm= 2>/dev/null || true)
             if [[ "$proc_cmd" == *python* ]] || [[ "$proc_cmd" == *uvicorn* ]]; then
-                log_step "Killing existing dashboard on port $DASHBOARD_PORT (PID: $existing_pid)..."
+                # Never kill a HEALTHY dashboard already serving here: it is almost
+                # always the user's own live dashboard (open in their browser), and
+                # killing it on `loki start` drops their session mid-use. A healthy
+                # server is reusable by this build too, so probe /api/status and, if
+                # it answers 200, REUSE it (skip starting our own). Only kill a
+                # dashboard process that is NOT serving (a genuinely stuck/dead one).
+                # Opt out with LOKI_DASHBOARD_FORCE_RECLAIM=1.
+                local _dash_alive=""
+                if [ "${LOKI_DASHBOARD_FORCE_RECLAIM:-}" != "1" ] && command -v curl >/dev/null 2>&1; then
+                    _dash_alive=$(curl -s -o /dev/null -w '%{http_code}' --max-time 1 \
+                        "http://127.0.0.1:${DASHBOARD_PORT}/api/status" 2>/dev/null || true)
+                fi
+                if [ "$_dash_alive" = "200" ]; then
+                    log_info "Reusing the healthy dashboard already serving on port $DASHBOARD_PORT (not killing it)."
+                    DASHBOARD_REUSED=1
+                    break
+                fi
+                log_step "Killing stuck dashboard on port $DASHBOARD_PORT (PID: $existing_pid, not serving)..."
                 kill "$existing_pid" 2>/dev/null || true
                 sleep 1
                 break
@@ -11260,6 +11294,15 @@ start_dashboard() {
         return 1
     fi
 
+    # If we found a HEALTHY dashboard already serving on the port, reuse it: do
+    # NOT launch a second server (that would fight for the port / kill the user's
+    # live one). The existing server already serves this project's state.
+    if [ "${DASHBOARD_REUSED:-0}" = "1" ]; then
+        export LOKI_DASHBOARD_PORT="$DASHBOARD_PORT"
+        log_info "Dashboard already live on port $DASHBOARD_PORT; reusing it."
+        return 0
+    fi
+
     # Start FastAPI dashboard server (unified UI + API)
     log_step "Starting unified dashboard server..."
     local log_file=".loki/dashboard/logs/dashboard.log"

package/dashboard/__init__.py

@@ -7,7 +7,7 @@ Modules:
     control: Session control API (start/stop/pause/resume)
 """
 
-__version__ = "7.98.0"
+__version__ = "7.99.1"
 
 # Expose the control app for easy import
 try:

package/dashboard/server.py

@@ -6240,9 +6240,14 @@ def _compute_cost_snapshot() -> dict:
     budget_used = 0.0
     budget_remaining = None
 
-    # Read efficiency files (one JSON file per iteration/task)
+    # Read efficiency files (one JSON file per iteration/task).
+    # Use the iteration-*.json pattern so this reader sees the same
+    # authoritative file set as _compute_budget_snapshot and
+    # _compute_cost_timeline (both glob iteration-*.json, mirroring
+    # check_budget_limit in run.sh). A bare *.json would also pick up
+    # non-iteration JSON in the dir and make the three cost readers disagree.
     if efficiency_dir.exists():
-        for eff_file in sorted(efficiency_dir.glob("*.json")):
+        for eff_file in sorted(efficiency_dir.glob("iteration-*.json")):
             try:
                 data = json.loads(eff_file.read_text())
                 # A corrupt/truncated efficiency file can parse to a non-object

package/docs/INSTALLATION.md

@@ -2,7 +2,7 @@
 
 The flagship product of [Autonomi](https://www.autonomi.dev/). Loki Mode is a spec-driven autonomous builder with a built-in trust layer that takes any spec to a deployed product and verifies completion with evidence (quality gates plus a completion council), not just a "done" claim. Complete installation instructions for all platforms and use cases.
 
-**Version:** v7.98.0
+**Version:** v7.99.1
 
 ---
 

package/loki-ts/dist/loki.js

@@ -1,5 +1,5 @@
 // @bun
-var z8=Object.defineProperty;var X8=($)=>$;function K8($,Q){this[$]=X8.bind(null,Q)}var b=($,Q)=>{for(var Z in Q)z8($,Z,{get:Q[Z],enumerable:!0,configurable:!0,set:K8.bind(Q,Z)})};var L=($,Q)=>()=>($&&(Q=$($=0)),Q);var J$=import.meta.require;var y1={};b(y1,{lokiDir:()=>P,homeLokiDir:()=>T$,findRepoRootForVersion:()=>e$,REPO_ROOT:()=>h});import{resolve as t,dirname as i$}from"path";import{fileURLToPath as q8}from"url";import{existsSync as E$}from"fs";import{homedir as J8}from"os";function V8(){let $=h1;for(let Q=0;Q<6;Q++){if(E$(t($,"VERSION"))&&E$(t($,"autonomy/run.sh")))return $;let Z=i$($);if(Z===$)break;$=Z}return t(h1,"..","..","..")}function e$($){let Q=$;for(let Z=0;Z<6;Z++){if(E$(t(Q,"VERSION"))&&E$(t(Q,"autonomy/run.sh")))return Q;let z=i$(Q);if(z===Q)break;Q=z}return t($,"..","..","..")}function P(){return process.env.LOKI_DIR??t(process.cwd(),".loki")}function T$(){return t(J8(),".loki")}var h1,h;var C=L(()=>{h1=i$(q8(import.meta.url));h=V8()});import{readFileSync as W8}from"fs";import{resolve as U8,dirname as H8}from"path";import{fileURLToPath as G8}from"url";function N$(){if(Q$!==null)return Q$;let $="7.98.0";if(typeof $==="string"&&$.length>0)return Q$=$,Q$;try{let Q=H8(G8(import.meta.url)),Z=e$(Q);Q$=W8(U8(Z,"VERSION"),"utf-8").trim()}catch{Q$="unknown"}return Q$}var Q$=null;var $1=L(()=>{C()});var u1={};b(u1,{runOrThrow:()=>x8,run:()=>F,readStreamCapped:()=>f1,commandVersion:()=>N8,commandExists:()=>f,ShellError:()=>Q1,MAX_STDOUT_BYTES:()=>m1});async function f1($,Q=m1){let Z=$.getReader(),z=new TextDecoder,X="",q=0;try{while(q<Q){let{done:K,value:W}=await Z.read();if(K)break;if(!W)continue;if(q+=W.byteLength,q>Q){let V=W.byteLength-(q-Q);X+=z.decode(W.subarray(0,V),{stream:!0});break}X+=z.decode(W,{stream:!0})}X+=z.decode()}finally{try{await Z.cancel()}catch{}Z.releaseLock()}return X}async function F($,Q={}){let Z=Bun.spawn({cmd:[...$],stdout:"pipe",stderr:"pipe",env:Q.env?{...process.env,...Q.env}:process.env,cwd:Q.cwd}),z,X;if(Q.timeoutMs&&Q.timeoutMs>0)z=setTimeout(()=>{try{Z.kill("SIGTERM")}catch{}X=setTimeout(()=>{try{Z.kill("SIGKILL")}catch{}},2000)},Q.timeoutMs);try{let[q,K,W]=await Promise.all([f1(Z.stdout),new Response(Z.stderr).text(),Z.exited]);return{stdout:q,stderr:K,exitCode:W}}finally{if(z)clearTimeout(z);if(X)clearTimeout(X)}}async function x8($,Q={}){let Z=await F($,Q);if(Z.exitCode!==0)throw new Q1(`command failed (${Z.exitCode}): ${$.join(" ")}`,Z.exitCode,Z.stdout,Z.stderr);return Z}async function f($){let Q=E8($),Z=await F(["sh","-c",`command -v ${Q}`],{timeoutMs:5000});if(Z.exitCode===0)return Z.stdout.trim()||null;return null}function E8($){if(!/^[A-Za-z0-9._/-]+$/.test($))throw Error(`refused to shell-escape suspect token: ${$}`);return $}async function N8($,Q="--version"){if(!await f($))return null;let z=await F([$,Q],{timeoutMs:5000});if(z.exitCode!==0)return null;return((z.stdout||z.stderr).split(/\r?\n/)[0]?.trim()??"")||null}var m1=16777216,Q1;var d=L(()=>{Q1=class Q1 extends Error{message;exitCode;stdout;stderr;constructor($,Q,Z,z){super($);this.message=$;this.exitCode=Q;this.stdout=Z;this.stderr=z;this.name="ShellError"}}});function r($){return S8?"":$}var S8,T,S,_,lZ,I,k,y,J;var c=L(()=>{S8=(process.env.NO_COLOR??"").length>0;T=r("\x1B[0;31m"),S=r("\x1B[0;32m"),_=r("\x1B[1;33m"),lZ=r("\x1B[0;34m"),I=r("\x1B[0;36m"),k=r("\x1B[1m"),y=r("\x1B[2m"),J=r("\x1B[0m")});import{existsSync as u8}from"fs";async function Z$(){if(A$!==void 0)return A$;let $="/opt/homebrew/bin/python3.12";if(u8($))return A$=$,$;let Q=await f("python3.12");if(Q)return A$=Q,Q;let Z=await f("python3");return A$=Z,Z}async function z$($,Q={}){let Z=await Z$();if(!Z)return{stdout:"",stderr:"python3 not found",exitCode:127};return F([Z,"-c",$],Q)}var A$;var V$=L(()=>{d()});var q0={};b(q0,{runStatus:()=>W3});import{existsSync as v,readFileSync as U$,readdirSync as i1,statSync as e1}from"fs";import{resolve as D,basename as $3}from"path";import{homedir as Q3}from"os";function $0($){let Q=Math.trunc($);if(Q>=1e6)return`${(Math.trunc(Q/1e6*10)/10).toFixed(1)}M`;if(Q>=1000)return`${(Math.trunc(Q/1000*10)/10).toFixed(1)}K`;return String(Q)}function Q0($,Q,Z){if(Q===0)return null;let z=Math.trunc($*100/Q),X=Math.trunc($*D$/Q);if(X>D$)X=D$;let q=D$-X,K=S;if(z>=80)K=T;else if(z>=50)K=_;let W="=".repeat(Math.max(0,X))+" ".repeat(Math.max(0,q)),V=$0($),U=$0(Q);return`  ${k}${Z}${J} ${K}[${W}]${J} ${z}% (${V} / ${U})`}async function z3(){if(await f("jq"))return!0;return process.stdout.write(`${T}Error: jq is required but not installed.${J}
+var z8=Object.defineProperty;var X8=($)=>$;function K8($,Q){this[$]=X8.bind(null,Q)}var b=($,Q)=>{for(var Z in Q)z8($,Z,{get:Q[Z],enumerable:!0,configurable:!0,set:K8.bind(Q,Z)})};var L=($,Q)=>()=>($&&(Q=$($=0)),Q);var J$=import.meta.require;var y1={};b(y1,{lokiDir:()=>P,homeLokiDir:()=>T$,findRepoRootForVersion:()=>e$,REPO_ROOT:()=>h});import{resolve as t,dirname as i$}from"path";import{fileURLToPath as q8}from"url";import{existsSync as E$}from"fs";import{homedir as J8}from"os";function V8(){let $=h1;for(let Q=0;Q<6;Q++){if(E$(t($,"VERSION"))&&E$(t($,"autonomy/run.sh")))return $;let Z=i$($);if(Z===$)break;$=Z}return t(h1,"..","..","..")}function e$($){let Q=$;for(let Z=0;Z<6;Z++){if(E$(t(Q,"VERSION"))&&E$(t(Q,"autonomy/run.sh")))return Q;let z=i$(Q);if(z===Q)break;Q=z}return t($,"..","..","..")}function P(){return process.env.LOKI_DIR??t(process.cwd(),".loki")}function T$(){return t(J8(),".loki")}var h1,h;var C=L(()=>{h1=i$(q8(import.meta.url));h=V8()});import{readFileSync as W8}from"fs";import{resolve as U8,dirname as H8}from"path";import{fileURLToPath as G8}from"url";function N$(){if(Q$!==null)return Q$;let $="7.99.1";if(typeof $==="string"&&$.length>0)return Q$=$,Q$;try{let Q=H8(G8(import.meta.url)),Z=e$(Q);Q$=W8(U8(Z,"VERSION"),"utf-8").trim()}catch{Q$="unknown"}return Q$}var Q$=null;var $1=L(()=>{C()});var u1={};b(u1,{runOrThrow:()=>x8,run:()=>F,readStreamCapped:()=>f1,commandVersion:()=>N8,commandExists:()=>f,ShellError:()=>Q1,MAX_STDOUT_BYTES:()=>m1});async function f1($,Q=m1){let Z=$.getReader(),z=new TextDecoder,X="",q=0;try{while(q<Q){let{done:K,value:W}=await Z.read();if(K)break;if(!W)continue;if(q+=W.byteLength,q>Q){let V=W.byteLength-(q-Q);X+=z.decode(W.subarray(0,V),{stream:!0});break}X+=z.decode(W,{stream:!0})}X+=z.decode()}finally{try{await Z.cancel()}catch{}Z.releaseLock()}return X}async function F($,Q={}){let Z=Bun.spawn({cmd:[...$],stdout:"pipe",stderr:"pipe",env:Q.env?{...process.env,...Q.env}:process.env,cwd:Q.cwd}),z,X;if(Q.timeoutMs&&Q.timeoutMs>0)z=setTimeout(()=>{try{Z.kill("SIGTERM")}catch{}X=setTimeout(()=>{try{Z.kill("SIGKILL")}catch{}},2000)},Q.timeoutMs);try{let[q,K,W]=await Promise.all([f1(Z.stdout),new Response(Z.stderr).text(),Z.exited]);return{stdout:q,stderr:K,exitCode:W}}finally{if(z)clearTimeout(z);if(X)clearTimeout(X)}}async function x8($,Q={}){let Z=await F($,Q);if(Z.exitCode!==0)throw new Q1(`command failed (${Z.exitCode}): ${$.join(" ")}`,Z.exitCode,Z.stdout,Z.stderr);return Z}async function f($){let Q=E8($),Z=await F(["sh","-c",`command -v ${Q}`],{timeoutMs:5000});if(Z.exitCode===0)return Z.stdout.trim()||null;return null}function E8($){if(!/^[A-Za-z0-9._/-]+$/.test($))throw Error(`refused to shell-escape suspect token: ${$}`);return $}async function N8($,Q="--version"){if(!await f($))return null;let z=await F([$,Q],{timeoutMs:5000});if(z.exitCode!==0)return null;return((z.stdout||z.stderr).split(/\r?\n/)[0]?.trim()??"")||null}var m1=16777216,Q1;var d=L(()=>{Q1=class Q1 extends Error{message;exitCode;stdout;stderr;constructor($,Q,Z,z){super($);this.message=$;this.exitCode=Q;this.stdout=Z;this.stderr=z;this.name="ShellError"}}});function r($){return S8?"":$}var S8,T,S,_,lZ,I,k,y,J;var c=L(()=>{S8=(process.env.NO_COLOR??"").length>0;T=r("\x1B[0;31m"),S=r("\x1B[0;32m"),_=r("\x1B[1;33m"),lZ=r("\x1B[0;34m"),I=r("\x1B[0;36m"),k=r("\x1B[1m"),y=r("\x1B[2m"),J=r("\x1B[0m")});import{existsSync as u8}from"fs";async function Z$(){if(A$!==void 0)return A$;let $="/opt/homebrew/bin/python3.12";if(u8($))return A$=$,$;let Q=await f("python3.12");if(Q)return A$=Q,Q;let Z=await f("python3");return A$=Z,Z}async function z$($,Q={}){let Z=await Z$();if(!Z)return{stdout:"",stderr:"python3 not found",exitCode:127};return F([Z,"-c",$],Q)}var A$;var V$=L(()=>{d()});var q0={};b(q0,{runStatus:()=>W3});import{existsSync as v,readFileSync as U$,readdirSync as i1,statSync as e1}from"fs";import{resolve as D,basename as $3}from"path";import{homedir as Q3}from"os";function $0($){let Q=Math.trunc($);if(Q>=1e6)return`${(Math.trunc(Q/1e6*10)/10).toFixed(1)}M`;if(Q>=1000)return`${(Math.trunc(Q/1000*10)/10).toFixed(1)}K`;return String(Q)}function Q0($,Q,Z){if(Q===0)return null;let z=Math.trunc($*100/Q),X=Math.trunc($*D$/Q);if(X>D$)X=D$;let q=D$-X,K=S;if(z>=80)K=T;else if(z>=50)K=_;let W="=".repeat(Math.max(0,X))+" ".repeat(Math.max(0,q)),V=$0($),U=$0(Q);return`  ${k}${Z}${J} ${K}[${W}]${J} ${z}% (${V} / ${U})`}async function z3(){if(await f("jq"))return!0;return process.stdout.write(`${T}Error: jq is required but not installed.${J}
 `),process.stdout.write(`Install with:
 `),process.stdout.write(`  brew install jq    (macOS)
 `),process.stdout.write(`  apt install jq     (Debian/Ubuntu)
@@ -802,4 +802,4 @@ Set LOKI_LEGACY_BASH=1 to force the bash CLI for every command.
 `),2}default:return process.stderr.write(`Unknown command: ${Q}
 `),process.stderr.write(Z8),2}}r1();process.on("SIGINT",()=>process.exit(130));process.on("SIGTERM",()=>process.exit(143));var FZ=await jZ(Bun.argv.slice(2));process.exit(FZ);
 
-//# debugId=5C332E0B9079B5FC64756E2164756E21
+//# debugId=2476B8BD9E98366964756E2164756E21

package/mcp/__init__.py

@@ -57,4 +57,4 @@ try:
 except ImportError:
     __all__ = ['mcp']
 
-__version__ = '7.98.0'
+__version__ = '7.99.1'

package/memory/retrieval.py

@@ -680,8 +680,10 @@ class MemoryRetrieval:
         for ns in namespaces:
             ns_retrieval = self.with_namespace(ns)
 
-            # Simple keyword search in this namespace
-            for collection in ["episodic", "semantic", "skills"]:
+            # Simple keyword search in this namespace.
+            # BUG-MEM-012: 'anti_patterns' was omitted, so anti-pattern
+            # memories were silently missed in cross-namespace search.
+            for collection in ["episodic", "semantic", "skills", "anti_patterns"]:
                 results = ns_retrieval.retrieve_by_keyword(
                     query.split(),
                     collection,
@@ -823,27 +825,55 @@ class MemoryRetrieval:
         if collection not in self.vector_indices:
             return self.retrieve_by_keyword(query.split(), collection)[:top_k]
 
-        # Check if indices need rebuilding after consolidation (BUG-MEM-002).
-        # If patterns.json was modified more recently than we last built
-        # indices, fall back to keyword search for accuracy.
-        if collection == "semantic" and self._indices_built_at is not None:
-            patterns_path = self.base_path / "semantic" / "patterns.json"
-            if patterns_path.exists():
+        # Check if indices need rebuilding after consolidation (BUG-MEM-002,
+        # BUG-MEM-007). Consolidation rewrites semantic/patterns.json (and may
+        # touch semantic/anti-patterns.json), so any index sourced from those
+        # files can go stale. The 'semantic' index reads patterns.json; the
+        # 'anti_patterns' index reads BOTH patterns.json and anti-patterns.json
+        # (consolidated anti-patterns are bridged from patterns.json). If a
+        # source file was modified more recently than we last built indices,
+        # fall back to keyword search for accuracy. (episodic/skills read their
+        # own per-record files and are not rewritten by consolidation, so they
+        # are not checked here.)
+        if self._indices_built_at is not None:
+            stale_sources: List[str] = []
+            if collection == "semantic":
+                stale_sources = ["semantic/patterns.json"]
+            elif collection == "anti_patterns":
+                stale_sources = ["semantic/patterns.json",
+                                 "semantic/anti-patterns.json"]
+            if stale_sources:
                 import os
-                patterns_mtime = os.path.getmtime(patterns_path)
-                if patterns_mtime > self._indices_built_at:
-                    logger.info(
-                        "Semantic index is stale (patterns modified after index build). "
-                        "Falling back to keyword search for accuracy."
-                    )
-                    return self.retrieve_by_keyword(query.split(), collection)[:top_k]
-
-        # Generate query embedding
-        query_embedding = self.embedding_engine.embed(query)
-
-        # Search vector index
+                for rel in stale_sources:
+                    source_path = self.base_path / rel
+                    if source_path.exists() and \
+                            os.path.getmtime(source_path) > self._indices_built_at:
+                        logger.info(
+                            "%s index is stale (%s modified after index build). "
+                            "Falling back to keyword search for accuracy.",
+                            collection, rel,
+                        )
+                        return self.retrieve_by_keyword(
+                            query.split(), collection)[:top_k]
+
+        # Generate query embedding and search the vector index. If the embedding
+        # engine has fallen back to a different model/dimension since the index
+        # was built, the query vector dimension will not match the stored index
+        # and VectorSearchIndex.search raises ValueError. That must NOT crash
+        # retrieval or return wrong-dimension neighbors -- degrade to keyword
+        # search (the honest, accurate fallback), same as the staleness path.
         index = self.vector_indices[collection]
-        results = index.search(query_embedding, top_k)
+        try:
+            query_embedding = self.embedding_engine.embed(query)
+            results = index.search(query_embedding, top_k)
+        except ValueError as exc:
+            logger.info(
+                "%s vector search failed (%s); likely an embedding "
+                "dimension change since index build. Falling back to keyword "
+                "search for accuracy.",
+                collection, exc,
+            )
+            return self.retrieve_by_keyword(query.split(), collection)[:top_k]
 
         # Convert to standard format
         items: List[Dict[str, Any]] = []
@@ -859,6 +889,34 @@ class MemoryRetrieval:
 
         return items
 
+    @staticmethod
+    def _anti_pattern_content_key(record: Dict[str, Any]) -> tuple:
+        """Normalized content key for an anti-pattern across both schemas.
+
+        Consolidation writes anti-patterns into semantic/patterns.json as
+        SemanticPattern objects (fields incorrect_approach|pattern /
+        description / correct_approach), while the legacy
+        semantic/anti-patterns.json uses what_fails / why / prevention. The
+        same anti-pattern can therefore appear in both stores (no migration
+        copies one into the other), which would double-count it on read and in
+        the vector index (BUG-MEM-011). Map both schemas onto the same
+        lowercased/stripped (what_fails, why, prevention) tuple so the two
+        representations of one anti-pattern collide on a single key.
+        """
+        def _norm(*candidates: Any) -> str:
+            for c in candidates:
+                if c:
+                    return str(c).strip().lower()
+            return ""
+
+        what_fails = _norm(record.get("what_fails"),
+                           record.get("incorrect_approach"),
+                           record.get("pattern"))
+        why = _norm(record.get("why"), record.get("description"))
+        prevention = _norm(record.get("prevention"),
+                           record.get("correct_approach"))
+        return (what_fails, why, prevention)
+
     @staticmethod
     def _parse_episode_timestamp(value: Any) -> Optional[datetime]:
         """Parse an episode timestamp to a tz-aware datetime, or None.
@@ -1746,6 +1804,25 @@ class MemoryRetrieval:
         """Keyword search in anti-patterns."""
         results: List[Dict[str, Any]] = []
         anti_data = self.storage.read_json("semantic/anti-patterns.json") or {}
+        patterns_data = self.storage.read_json("semantic/patterns.json") or {}
+
+        # BUG-MEM-011: an anti-pattern can live in BOTH the consolidated
+        # patterns.json (category="anti-pattern") and the legacy
+        # anti-patterns.json, with no migration copying one into the other.
+        # Reading both naively double-counts it. Pre-scan the consolidated
+        # store (which we keep) into a seen-set keyed by id AND normalized
+        # content, then skip any legacy record that collides with either.
+        seen_ids: set = set()
+        seen_content: set = set()
+        for pat in patterns_data.get("patterns", []):
+            if not isinstance(pat, dict):
+                continue
+            if pat.get("category") != "anti-pattern":
+                continue
+            pid = pat.get("id")
+            if pid:
+                seen_ids.add(pid)
+            seen_content.add(self._anti_pattern_content_key(pat))
 
         for anti in anti_data.get("anti_patterns", []):
             # Defensive: mirror the sibling loop below. A corrupt or
@@ -1753,6 +1830,11 @@ class MemoryRetrieval:
             # the isinstance guard and (x or "") avoid AttributeError.
             if not isinstance(anti, dict):
                 continue
+            # Dedup: skip a legacy record already represented in patterns.json.
+            aid = anti.get("id")
+            if (aid and aid in seen_ids) or \
+                    self._anti_pattern_content_key(anti) in seen_content:
+                continue
             what_fails = (anti.get("what_fails") or "").lower()
             why = (anti.get("why") or "").lower()
             prevention = (anti.get("prevention") or "").lower()
@@ -1774,7 +1856,6 @@ class MemoryRetrieval:
         # description / correct_approach. Without this bridge, consolidated
         # anti-patterns were never retrievable. Map them onto the same
         # what_fails / why / prevention scoring shape.
-        patterns_data = self.storage.read_json("semantic/patterns.json") or {}
         for pat in patterns_data.get("patterns", []):
             if not isinstance(pat, dict):
                 continue
@@ -1888,8 +1969,33 @@ class MemoryRetrieval:
 
         index = self.vector_indices["anti_patterns"]
         anti_data = self.storage.read_json("semantic/anti-patterns.json") or {}
+        patterns_data = self.storage.read_json("semantic/patterns.json") or {}
+
+        # BUG-MEM-011: the same anti-pattern may live in BOTH the consolidated
+        # patterns.json and the legacy anti-patterns.json. Indexing both
+        # double-counts it in the vector index. Pre-scan the consolidated store
+        # (which we keep) into a seen-set keyed by id AND normalized content,
+        # then skip any legacy record that collides with either.
+        seen_ids: set = set()
+        seen_content: set = set()
+        for pat in patterns_data.get("patterns", []):
+            if not isinstance(pat, dict):
+                continue
+            if pat.get("category") != "anti-pattern":
+                continue
+            pid = pat.get("id")
+            if pid:
+                seen_ids.add(pid)
+            seen_content.add(self._anti_pattern_content_key(pat))
 
         for anti in anti_data.get("anti_patterns", []):
+            if not isinstance(anti, dict):
+                continue
+            # Dedup: skip a legacy record already represented in patterns.json.
+            aid = anti.get("id")
+            if (aid and aid in seen_ids) or \
+                    self._anti_pattern_content_key(anti) in seen_content:
+                continue
             # Create text for embedding
             text = f"{anti.get('what_fails', '')} {anti.get('why', '')} {anti.get('prevention', '')}"
 
@@ -1904,7 +2010,6 @@ class MemoryRetrieval:
         # category="anti-pattern" entries in semantic/patterns.json, not the
         # legacy anti-patterns.json above. Bridge those into the vector index
         # too so embedding-based retrieval sees consolidated anti-patterns.
-        patterns_data = self.storage.read_json("semantic/patterns.json") or {}
         for pat in patterns_data.get("patterns", []):
             if not isinstance(pat, dict):
                 continue

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "loki-mode",
   "mcpName": "io.github.asklokesh/loki-mode",
-  "version": "7.98.0",
+  "version": "7.99.1",
   "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": "7.98.0",
+  "version": "7.99.1",
   "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",