@phren/cli 0.0.32 → 0.0.34

package/mcp/dist/shared/index.js

@@ -17,7 +17,7 @@ import { buildSourceDocKey, queryDocBySourceKey, queryDocRows, } from "../index-
 import { classifyTopicForText, readProjectTopics, } from "../project-topics.js";
 export { porterStem } from "./stemmer.js";
 export { cosineFallback } from "./search-fallback.js";
-export { queryFragmentLinks, queryFragmentLinks as queryEntityLinks, getFragmentBoostDocs, getFragmentBoostDocs as getEntityBoostDocs, ensureGlobalEntitiesTable, queryCrossProjectFragments, logFragmentMiss, logFragmentMiss as logEntityMiss, extractFragmentNames, extractFragmentNames as extractEntityNames, } from "./fragment-graph.js";
+export { queryFragmentLinks, getFragmentBoostDocs, ensureGlobalEntitiesTable, queryCrossProjectFragments, logFragmentMiss, extractFragmentNames, } from "./fragment-graph.js";
 export { buildSourceDocKey, decodeFiniteNumber, decodeStringRow, extractSnippet, getDocSourceKey, normalizeMemoryId, queryDocBySourceKey, queryDocRows, queryRows, rowToDoc, rowToDocWithRowid, } from "../index-query.js";
 // ── Async embedding queue ───────────────────────────────────────────────────
 const _embQueue = new Map();
@@ -165,6 +165,7 @@ function _resolveImportsRecursive(content, phrenPath, seen, depth) {
  * The import path is resolved relative to the phren root (e.g. `shared/foo.md` -> `~/.phren/global/shared/foo.md`).
  * Circular imports are detected and skipped. Depth is capped to prevent runaway recursion.
  */
+/** @internal Exported for tests. */
 export function resolveImports(content, phrenPath) {
     return _resolveImportsRecursive(content, phrenPath, new Set(), 0);
 }
@@ -324,7 +325,7 @@ function loadHashMap(phrenPath) {
     }
     return { hashes: {} };
 }
-function saveHashMap(phrenPath, hashes) {
+function saveHashMap(phrenPath, hashes, knownPaths) {
     const runtimeDir = path.join(phrenPath, ".runtime");
     try {
         fs.mkdirSync(runtimeDir, { recursive: true });
@@ -343,9 +344,11 @@ function saveHashMap(phrenPath, hashes) {
                 logger.debug("saveHashMap readExisting", errorMessage(err));
             }
             const merged = { ...existing, ...hashes };
-            // Remove entries for paths that no longer exist on disk
+            // Remove entries for paths that no longer exist. When knownPaths is provided
+            // (build passes supply the full file list), use set membership instead of
+            // hitting the filesystem — avoids N sync stat calls inside the lock.
             for (const filePath of Object.keys(merged)) {
-                if (!fs.existsSync(filePath)) {
+                if (knownPaths ? !knownPaths.has(filePath) : !fs.existsSync(filePath)) {
                     delete merged[filePath];
                 }
             }
@@ -815,7 +818,8 @@ function mergeManualLinks(db, phrenPath) {
 }
 async function buildIndexImpl(phrenPath, profile) {
     const t0 = Date.now();
-    beginUserFragmentBuildCache(phrenPath, getProjectDirs(phrenPath, profile).map(dir => path.basename(dir)));
+    const projectDirs = getProjectDirs(phrenPath, profile);
+    beginUserFragmentBuildCache(phrenPath, projectDirs.map(dir => path.basename(dir)));
     try {
         // ── Cache dir + hash sentinel ─────────────────────────────────────────────
         let userSuffix;
@@ -1021,7 +1025,7 @@ async function buildIndexImpl(phrenPath, profile) {
                                 throw err;
                             }
                         }
-                        saveHashMap(phrenPath, currentHashes);
+                        saveHashMap(phrenPath, currentHashes, new Set(Object.keys(currentHashes)));
                         touchSentinel(phrenPath);
                         invalidateDfCache();
                         // Save updated cache
@@ -1120,19 +1124,19 @@ async function buildIndexImpl(phrenPath, profile) {
         // Always merge manual links (survive rebuild)
         mergeManualLinks(db, phrenPath);
         // ── Finalize: persist hashes, save cache, log ─────────────────────────────
-        saveHashMap(phrenPath, newHashes);
+        saveHashMap(phrenPath, newHashes, new Set(Object.keys(newHashes)));
         touchSentinel(phrenPath);
         invalidateDfCache();
         const buildMs = Date.now() - t0;
-        debugLog(`Built FTS index: ${fileCount} files from ${getProjectDirs(phrenPath, profile).length} projects in ${buildMs}ms`);
+        debugLog(`Built FTS index: ${fileCount} files from ${projectDirs.length} projects in ${buildMs}ms`);
         if ((process.env.PHREN_DEBUG))
-            console.error(`Indexed ${fileCount} files from ${getProjectDirs(phrenPath, profile).length} projects`);
+            console.error(`Indexed ${fileCount} files from ${projectDirs.length} projects`);
         appendIndexEvent(phrenPath, {
             event: "build_index",
             cache: "miss",
             hash: hash.slice(0, 12),
             files: fileCount,
-            projects: getProjectDirs(phrenPath, profile).length,
+            projects: projectDirs.length,
             elapsedMs: buildMs,
             profile: profile || "",
         });

package/mcp/dist/shared/ollama.js

@@ -3,6 +3,11 @@ const DEFAULT_OLLAMA_URL = "http://localhost:11434";
 const DEFAULT_EMBEDDING_MODEL = "nomic-embed-text";
 const DEFAULT_EXTRACT_MODEL = "llama3.2";
 const MAX_EMBED_INPUT_CHARS = 6000;
+const CLOUD_EMBEDDING_TIMEOUT_MS = 15_000;
+const OLLAMA_HEALTH_TIMEOUT_MS = 2_000;
+const OLLAMA_EMBEDDING_TIMEOUT_MS = 10_000;
+const OLLAMA_GENERATE_TIMEOUT_MS = 60_000;
+/** @internal Exported for tests. */
 export function prepareEmbeddingInput(text) {
     return text
         .replace(/<!--[\s\S]*?-->/g, " ")
@@ -44,7 +49,7 @@ async function embedTextCloud(input, baseUrl, model, apiKey) {
         headers["Authorization"] = `Bearer ${apiKey}`;
     try {
         const controller = new AbortController();
-        const id = setTimeout(() => controller.abort(), 15000);
+        const id = setTimeout(() => controller.abort(), CLOUD_EMBEDDING_TIMEOUT_MS);
         const res = await fetch(`${baseUrl}/embeddings`, {
             method: "POST",
             headers,
@@ -85,7 +90,7 @@ export async function checkOllamaAvailable(url) {
         return false;
     try {
         const controller = new AbortController();
-        const id = setTimeout(() => controller.abort(), 2000);
+        const id = setTimeout(() => controller.abort(), OLLAMA_HEALTH_TIMEOUT_MS);
         const res = await fetch(`${baseUrl}/api/tags`, { signal: controller.signal });
         clearTimeout(id);
         return res.ok;
@@ -104,7 +109,7 @@ export async function checkModelAvailable(model, url) {
     const modelName = model ?? getEmbeddingModel();
     try {
         const controller = new AbortController();
-        const id = setTimeout(() => controller.abort(), 2000);
+        const id = setTimeout(() => controller.abort(), OLLAMA_HEALTH_TIMEOUT_MS);
         const res = await fetch(`${baseUrl}/api/tags`, { signal: controller.signal });
         clearTimeout(id);
         if (!res.ok)
@@ -131,7 +136,7 @@ export async function embedText(text, model, url) {
         return null;
     try {
         const controller = new AbortController();
-        const id = setTimeout(() => controller.abort(), 10000);
+        const id = setTimeout(() => controller.abort(), OLLAMA_EMBEDDING_TIMEOUT_MS);
         const res = await fetch(`${baseUrl}/api/embed`, {
             method: "POST",
             headers: { "Content-Type": "application/json" },
@@ -158,7 +163,7 @@ export async function generateText(prompt, model, url) {
     const modelName = model ?? getExtractModel();
     try {
         const controller = new AbortController();
-        const id = setTimeout(() => controller.abort(), 60000);
+        const id = setTimeout(() => controller.abort(), OLLAMA_GENERATE_TIMEOUT_MS);
         const res = await fetch(`${baseUrl}/api/generate`, {
             method: "POST",
             headers: { "Content-Type": "application/json" },
@@ -178,4 +183,17 @@ export async function generateText(prompt, model, url) {
         return null;
     }
 }
+/**
+ * Probe Ollama availability and model readiness in one call.
+ * Returns a status enum so callers can branch on it without repeating the check logic.
+ */
+export async function checkOllamaStatus() {
+    if (!getOllamaUrl())
+        return "disabled";
+    const ollamaUp = await checkOllamaAvailable();
+    if (!ollamaUp)
+        return "not_running";
+    const modelReady = await checkModelAvailable();
+    return modelReady ? "ready" : "no_model";
+}
 export { cosineSimilarity } from "../embedding.js";

package/mcp/dist/shared/process.js

@@ -0,0 +1,24 @@
+/**
+ * Shared process helpers for spawning detached child processes.
+ */
+import { spawn } from "child_process";
+import { resolveRuntimeProfile } from "../runtime-profile.js";
+/**
+ * Spawn a detached child process with the standard phren environment.
+ * When logFd is provided, stdout/stderr are redirected to that fd.
+ * When omitted, all stdio is ignored.
+ * Returns the ChildProcess so callers can attach `.unref()` or `.on("exit", ...)`.
+ */
+export function spawnDetachedChild(args, opts) {
+    return spawn(process.execPath, args, {
+        cwd: opts.cwd ?? process.cwd(),
+        detached: true,
+        stdio: opts.logFd !== undefined ? ["ignore", opts.logFd, opts.logFd] : "ignore",
+        env: {
+            ...process.env,
+            PHREN_PATH: opts.phrenPath,
+            PHREN_PROFILE: resolveRuntimeProfile(opts.phrenPath),
+            ...opts.extraEnv,
+        },
+    });
+}

package/mcp/dist/shared/retrieval.js

@@ -1,6 +1,6 @@
 // shared-retrieval.ts — shared retrieval core used by hooks and MCP search.
 import { getQualityMultiplier, entryScoreKey, } from "./governance.js";
-import { queryDocRows, queryRows, cosineFallback, extractSnippet, getDocSourceKey, getEntityBoostDocs, decodeFiniteNumber, rowToDocWithRowid, buildIndex, } from "./index.js";
+import { queryDocRows, queryRows, cosineFallback, extractSnippet, getDocSourceKey, getFragmentBoostDocs, decodeFiniteNumber, rowToDocWithRowid, buildIndex, } from "./index.js";
 import { filterTrustedFindingsDetailed, } from "./content.js";
 import { parseCitationComment } from "../content/citation.js";
 import { getHighImpactFindings } from "../finding/impact.js";
@@ -183,6 +183,7 @@ const RRF_K = 60;
  * Documents appearing in multiple tiers get a higher combined score.
  * Formula: score(d) = Σ 1/(k + rank_i) for each tier i containing d, where k=60 (standard).
  */
+/** @internal Exported for tests. */
 export function rrfMerge(tiers, k = RRF_K) {
     const scores = new Map();
     const docs = new Map();
@@ -267,6 +268,7 @@ function semanticFallbackDocs(db, prompt, project) {
         .map((x) => x.doc);
     return scored;
 }
+/** @internal Exported for tests. */
 export function shouldRunVectorExpansion(rows, prompt, desiredResults = VECTOR_FALLBACK_SKIP_COUNT) {
     if (!rows || rows.length === 0)
         return true;
@@ -492,7 +494,7 @@ export async function searchKnowledgeRows(db, options) {
  * Parse PHREN_FEDERATION_PATHS env var and return valid, distinct paths.
  * Paths are colon-separated. The local phrenPath is excluded to avoid duplicate results.
  */
-export function parseFederationPaths(localPhrenPath) {
+function parseFederationPaths(localPhrenPath) {
     const raw = process.env.PHREN_FEDERATION_PATHS ?? "";
     if (!raw.trim())
         return [];
@@ -624,7 +626,7 @@ export function rankResults(rows, intent, gitCtx, detectedProject, phrenPathLoca
         if (canonicalRows)
             ranked = [...canonicalRows, ...ranked];
     }
-    const entityBoost = query ? getEntityBoostDocs(db, query) : new Set();
+    const entityBoost = query ? getFragmentBoostDocs(db, query) : new Set();
     const entityBoostPaths = new Set();
     for (const doc of ranked) {
         // Use getDocSourceKey to build the full project/relFile key, matching what
@@ -735,7 +737,8 @@ export function rankResults(rows, intent, gitCtx, detectedProject, phrenPathLoca
     }
     return ranked;
 }
-/** Mark snippet lines with stale citations (cited file missing or line content changed). */
+/** Mark snippet lines with stale citations (cited file missing or line content changed).
+ * @internal Exported for tests. */
 export function markStaleCitations(snippet) {
     const lines = snippet.split("\n");
     const result = [];

package/mcp/dist/shared/search-fallback.js

@@ -17,6 +17,7 @@ const COSINE_WINDOW_COUNT = 4;
 function splitPathSegments(filePath) {
     return filePath.split(/[\\/]+/).filter(Boolean);
 }
+/** @internal Exported for tests. */
 export function deriveVectorDocIdentity(phrenPath, fullPath) {
     const normalizedPhrenPath = phrenPath.replace(/[\\/]+/g, "/").replace(/\/+$/, "");
     const normalizedFullPath = fullPath.replace(/[\\/]+/g, "/");

package/mcp/dist/shared.js

@@ -3,6 +3,7 @@ import * as path from "path";
 import { debugLog, runtimeFile } from "./phren-paths.js";
 import { errorMessage } from "./utils.js";
 import { withFileLock } from "./governance/locks.js";
+const MAX_LOG_LINES = 1000;
 export { HOOK_TOOL_NAMES, hookConfigPath } from "./provider-adapters.js";
 export { EXEC_TIMEOUT_MS, EXEC_TIMEOUT_QUICK_MS, PhrenError, phrenOk, phrenErr, forwardErr, parsePhrenErrorCode, isRecord, withDefaults, FINDING_TYPES, FINDING_TAGS, KNOWN_OBSERVATION_TAGS, DOC_TYPES, capCache, RESERVED_PROJECT_DIR_NAMES, } from "./phren-core.js";
 export { ROOT_MANIFEST_FILENAME, homeDir, homePath, expandHomePath, defaultPhrenPath, rootManifestPath, readRootManifest, writeRootManifest, resolveInstallContext, findNearestPhrenPath, isProjectLocalMode, runtimeDir, tryUnlink, sessionsDir, runtimeFile, installPreferencesFile, runtimeHealthFile, shellStateFile, sessionMetricsFile, memoryScoresFile, memoryUsageLogFile, sessionMarker, debugLog, appendIndexEvent, resolveFindingsPath, findPhrenPath, ensurePhrenPath, findPhrenPathWithArg, normalizeProjectNameForCreate, findProjectNameCaseInsensitive, findArchivedProjectNameCaseInsensitive, getProjectDirs, collectNativeMemoryFiles, computePhrenLiveStateToken, getPhrenPath, qualityMarkers, atomicWriteText, } from "./phren-paths.js";
@@ -39,7 +40,7 @@ export function appendAuditLog(phrenPath, event, details) {
             if (stat.size > 1_000_000) {
                 const content = fs.readFileSync(logPath, "utf8");
                 const lines = content.split("\n");
-                fs.writeFileSync(logPath, lines.slice(-500).join("\n") + "\n");
+                fs.writeFileSync(logPath, lines.slice(-MAX_LOG_LINES).join("\n") + "\n");
             }
         });
     }

package/mcp/dist/shell/render.js

@@ -37,7 +37,7 @@ export function separator(width = 50) {
 export function stripAnsi(s) {
     return s.replace(/\x1b\[[0-9;?]*[ -/]*[@-~]/g, "");
 }
-export function visibleWidth(s) {
+function visibleWidth(s) {
     return stripAnsi(s).length;
 }
 export function padToWidth(s, width) {

package/mcp/dist/skill/registry.js

@@ -223,7 +223,7 @@ export function getAllSkills(phrenPath, profile) {
     }
     return all;
 }
-export function getLocalSkills(phrenPath, scope) {
+function getLocalSkills(phrenPath, scope) {
     if (scope.toLowerCase() === "global")
         return getGlobalSkills(phrenPath);
     return getProjectLocalSkills(phrenPath, scope);

package/mcp/dist/skill/state.js

@@ -23,6 +23,3 @@ export function setSkillEnabled(phrenPath, scope, name, enabled) {
         disabledSkills: Object.keys(disabled).length ? disabled : undefined,
     });
 }
-export function getSkillStateKey(scope, name) {
-    return skillStateKey(scope, name);
-}

package/mcp/dist/task/github.js

@@ -16,6 +16,7 @@ export function parseGithubIssueUrl(url) {
         url: match[0],
     };
 }
+/** @internal Exported for tests. */
 export function extractGithubRepoFromText(content) {
     const match = content.match(GITHUB_REPO_URL);
     return match?.[1];

package/mcp/dist/task/lifecycle.js

@@ -80,7 +80,7 @@ function clearTaskSessionState(phrenPath, sessionId) {
         debugLog(`task lifecycle clear session ${sessionId}: ${errorMessage(err)}`);
     }
 }
-export function getTaskMode(phrenPath) {
+function getTaskMode(phrenPath) {
     return getWorkflowPolicy(phrenPath).taskMode;
 }
 function isActionablePrompt(prompt, intent) {
@@ -330,11 +330,6 @@ export function finalizeTaskSession(args) {
         return;
     }
 }
-export function clearTaskSession(phrenPath, sessionId) {
-    if (!sessionId)
-        return;
-    clearTaskSessionState(phrenPath, sessionId);
-}
 /**
  * Return the active TaskItem tracked for a session+project, if any.
  * Used by mcp-finding.ts to link findings to active tasks.