@phren/cli 0.0.28 → 0.0.33

package/mcp/dist/{shared-ollama.js → shared/ollama.js}

@@ -1,8 +1,13 @@
-import { debugLog } from "./shared.js";
+import { debugLog } from "../shared.js";
 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;
     }
 }
-export { cosineSimilarity } from "./embedding.js";
+/**
+ * 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 → shared/retrieval.js}

@@ -1,17 +1,18 @@
 // shared-retrieval.ts — shared retrieval core used by hooks and MCP search.
-import { getQualityMultiplier, entryScoreKey, } from "./shared-governance.js";
-import { queryDocRows, queryRows, cosineFallback, extractSnippet, getDocSourceKey, getEntityBoostDocs, decodeFiniteNumber, rowToDocWithRowid, buildIndex, } from "./shared-index.js";
-import { filterTrustedFindingsDetailed, } from "./shared-content.js";
-import { parseCitationComment } from "./content-citation.js";
-import { getHighImpactFindings } from "./finding-impact.js";
-import { buildFtsQueryVariants, buildRelaxedFtsQuery, isFeatureEnabled, STOP_WORDS, errorMessage } from "./utils.js";
+import { getQualityMultiplier, entryScoreKey, } from "./governance.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";
+import { buildFtsQueryVariants, buildRelaxedFtsQuery, isFeatureEnabled, STOP_WORDS, errorMessage } from "../utils.js";
+import { logger } from "../logger.js";
 import * as fs from "fs";
 import * as path from "path";
-import { getProjectGlobBoost } from "./cli-hooks-globs.js";
-import { vectorFallback, deterministicSeed } from "./shared-search-fallback.js";
-import { getOllamaUrl, getCloudEmbeddingUrl } from "./shared-ollama.js";
-import { keywordFallbackSearch } from "./core-search.js";
-import { debugLog } from "./shared.js";
+import { getProjectGlobBoost } from "../cli/hooks-globs.js";
+import { vectorFallback, deterministicSeed } from "./search-fallback.js";
+import { getOllamaUrl, getCloudEmbeddingUrl } from "./ollama.js";
+import { keywordFallbackSearch } from "../core/search.js";
+import { debugLog } from "../shared.js";
 // ── Scoring constants ─────────────────────────────────────────────────────────
 /** Number of docs sampled for token-overlap semantic fallback search. */
 const SEMANTIC_FALLBACK_SAMPLE_LIMIT = 100;
@@ -182,6 +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();
@@ -266,6 +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;
@@ -383,8 +386,7 @@ export async function searchDocumentsAsync(db, safeQuery, prompt, keywords, dete
     }
     catch (err) {
         // Vector search failure is non-fatal — return sync result
-        if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] hybridSearch vectorFallback: ${errorMessage(err)}\n`);
+        logger.debug("hybridSearch vectorFallback", errorMessage(err));
         return syncResult;
     }
 }
@@ -483,9 +485,7 @@ export async function searchKnowledgeRows(db, options) {
             }
         }
         catch (err) {
-            if ((process.env.PHREN_DEBUG)) {
-                process.stderr.write(`[phren] vectorFallback: ${errorMessage(err)}\n`);
-            }
+            logger.debug("vectorFallback", errorMessage(err));
         }
     }
     return { safeQuery, rows, usedFallback };
@@ -494,7 +494,7 @@ export async function searchKnowledgeRows(db, options) {
  * Parse PHREN_FEDERATION_PATHS env var and return valid, distinct paths.
  * Paths are colon-separated. The local phrenPath is excluded to avoid duplicate results.
  */
-export function parseFederationPaths(localPhrenPath) {
+function parseFederationPaths(localPhrenPath) {
     const raw = process.env.PHREN_FEDERATION_PATHS ?? "";
     if (!raw.trim())
         return [];
@@ -523,9 +523,7 @@ export async function searchFederatedStores(localPhrenPath, options) {
             }
         }
         catch (err) {
-            if (process.env.PHREN_DEBUG) {
-                process.stderr.write(`[phren] federatedSearch storePath=${storePath}: ${errorMessage(err)}\n`);
-            }
+            logger.debug(`federatedSearch storePath=${storePath}`, errorMessage(err));
             // Federation errors are non-fatal — continue with other stores
         }
     }
@@ -628,7 +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
@@ -739,7 +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 = [];
@@ -771,8 +770,7 @@ export function markStaleCitations(snippet) {
                             }
                         }
                         catch (err) {
-                            if ((process.env.PHREN_DEBUG))
-                                process.stderr.write(`[phren] applyCitationAnnotations fileRead: ${errorMessage(err)}\n`);
+                            logger.debug("applyCitationAnnotations fileRead", errorMessage(err));
                             stale = true;
                         }
                     }

package/mcp/dist/{shared-search-fallback.js → shared/search-fallback.js}

@@ -1,11 +1,12 @@
 import { createHash } from "crypto";
-import { debugLog } from "./shared.js";
-import { STOP_WORDS, errorMessage } from "./utils.js";
-import { porterStem } from "./shared-stemmer.js";
-import { classifyFile, normalizeIndexedContent, rowToDocWithRowid } from "./shared-index.js";
-import { embedText, cosineSimilarity, getEmbeddingModel, getOllamaUrl, getCloudEmbeddingUrl } from "./shared-ollama.js";
-import { getEmbeddingCache } from "./shared-embedding-cache.js";
-import { getPersistentVectorIndex } from "./shared-vector-index.js";
+import { debugLog } from "../shared.js";
+import { logger } from "../logger.js";
+import { STOP_WORDS, errorMessage } from "../utils.js";
+import { porterStem } from "./stemmer.js";
+import { classifyFile, normalizeIndexedContent, rowToDocWithRowid } from "./index.js";
+import { embedText, cosineSimilarity, getEmbeddingModel, getOllamaUrl, getCloudEmbeddingUrl } from "./ollama.js";
+import { getEmbeddingCache } from "./embedding-cache.js";
+import { getPersistentVectorIndex } from "./vector-index.js";
 import * as fs from "fs";
 import * as path from "path";
 const HYBRID_SEARCH_FLAG = "PHREN_FEATURE_HYBRID_SEARCH";
@@ -16,6 +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(/\/+$/, "");
     const normalizedFullPath = fullPath.replace(/[\\/]+/g, "/");
@@ -123,8 +125,10 @@ function tfidfCosine(docs, query, corpusN) {
     const N = corpusN ?? docs.length;
     // Compute document frequency for each term, keyed by a fingerprint of the candidate doc set
     // so that different subsets and incremental index mutations get distinct cache entries.
+    const corpusSize = docTokenLists.length;
+    const corpusLengthSum = docTokenLists.reduce((sum, tl) => sum + tl.length, 0);
     const candidateFingerprint = docTokenLists.map(tl => tl.slice(0, 4).join(",")).join("|").slice(0, 128);
-    const cacheKey = `fp:${candidateFingerprint}`;
+    const cacheKey = `fp:${corpusSize}:${corpusLengthSum}:${candidateFingerprint}`;
     const cachedDf = dfCache.get(cacheKey);
     const df = cachedDf ?? new Map();
     // Compute DF for any terms not yet in cache
@@ -181,8 +185,7 @@ export function cosineFallback(db, query, excludeRowids, limit) {
         }
     }
     catch (err) {
-        if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] cosineFallback count: ${errorMessage(err)}\n`);
+        logger.debug("cosineFallback count", errorMessage(err));
         return [];
     }
     if (totalDocs > COSINE_MAX_CORPUS) {
@@ -210,8 +213,7 @@ export function cosineFallback(db, query, excludeRowids, limit) {
                         ftsRows.push(...ftsRes[0].values);
                 }
                 catch (err) {
-                    if ((process.env.PHREN_DEBUG))
-                        process.stderr.write(`[phren] cosineFallback FTS pre-filter: ${errorMessage(err)}\n`);
+                    logger.debug("cosineFallback FTS pre-filter", errorMessage(err));
                 }
             }
             // If FTS gave fewer than cap, supplement with deterministic rowid windows.
@@ -248,8 +250,7 @@ export function cosineFallback(db, query, excludeRowids, limit) {
                     }
                 }
                 catch (err) {
-                    if ((process.env.PHREN_DEBUG))
-                        process.stderr.write(`[phren] cosineFallback deterministicSample: ${errorMessage(err)}\n`);
+                    logger.debug("cosineFallback deterministicSample", errorMessage(err));
                 }
             }
             if (ftsRows.length === 0)
@@ -259,8 +260,7 @@ export function cosineFallback(db, query, excludeRowids, limit) {
         }
     }
     catch (err) {
-        if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] cosineFallback loadDocs: ${errorMessage(err)}\n`);
+        logger.debug("cosineFallback loadDocs", errorMessage(err));
         return [];
     }
     // Separate rowids, DocRows, and content strings for scoring
@@ -305,8 +305,7 @@ export async function vectorFallback(phrenPath, query, excludePaths, limit, proj
             await cache.load();
         }
         catch (err) {
-            if ((process.env.PHREN_DEBUG))
-                process.stderr.write(`[phren] vectorFallback cacheLoad: ${errorMessage(err)}\n`);
+            logger.debug("vectorFallback cacheLoad", errorMessage(err));
         }
     }
     if (cache.size() === 0)
@@ -357,8 +356,7 @@ export async function vectorFallback(phrenPath, query, excludePaths, limit, proj
             }
         }
         catch (err) {
-            if ((process.env.PHREN_DEBUG))
-                process.stderr.write(`[phren] vectorFallback fileRead: ${errorMessage(err)}\n`);
+            logger.debug("vectorFallback fileRead", errorMessage(err));
         }
         return { project: entryProject, filename, type, content, path: e.path };
     });

package/mcp/dist/{shared-sqljs.js → shared/sqljs.js}

@@ -2,7 +2,8 @@ import * as fs from "fs";
 import * as path from "path";
 import { fileURLToPath } from "url";
 import { createRequire } from "module";
-import { errorMessage } from "./utils.js";
+import { errorMessage } from "../utils.js";
+import { logger } from "../logger.js";
 const require = createRequire(import.meta.url);
 /**
  * Locate the sql.js-fts5 WASM binary by require.resolve with path-probe fallback.
@@ -15,8 +16,7 @@ function findWasmBinary() {
             return fs.readFileSync(resolved);
     }
     catch (err) {
-        if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] findWasmBinary requireResolve: ${errorMessage(err)}\n`);
+        logger.debug("sqljs", `findWasmBinary requireResolve: ${errorMessage(err)}`);
         // fall through to path probing
     }
     const __filename = fileURLToPath(import.meta.url);

package/mcp/dist/{shared-vector-index.js → shared/vector-index.js}

@@ -1,8 +1,8 @@
 import * as fs from "fs";
 import * as crypto from "crypto";
-import { runtimeFile, debugLog } from "./shared.js";
-import { withFileLock } from "./shared-governance.js";
-import { errorMessage } from "./utils.js";
+import { runtimeFile, debugLog } from "../shared.js";
+import { withFileLock } from "./governance.js";
+import { errorMessage } from "../utils.js";
 const VECTOR_INDEX_VERSION = 1;
 const VECTOR_INDEX_TABLE_COUNT = 4;
 const VECTOR_INDEX_BITS_PER_TABLE = 12;

package/mcp/dist/shared.js

@@ -2,6 +2,8 @@ import * as fs from "fs";
 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";
@@ -30,75 +32,19 @@ export function impactLogFile(phrenPath) {
 export function appendAuditLog(phrenPath, event, details) {
     const logPath = runtimeFile(phrenPath, "audit.log");
     const line = `[${new Date().toISOString()}] ${event} ${details}\n`;
-    const lockPath = logPath + ".lock";
-    const maxWait = 5000;
-    const pollMs = 50;
-    const staleMs = 30_000;
-    const waiter = new Int32Array(new SharedArrayBuffer(4));
-    // Q82: use an inline lock (same protocol as withFileLock) to guard the
-    // append + conditional rotation so concurrent processes don't read the same
-    // old content and race to write a truncated version each.
-    let waited = 0;
-    let hasLock = false;
     try {
-        fs.mkdirSync(path.dirname(lockPath), { recursive: true });
-        while (waited < maxWait) {
-            try {
-                fs.writeFileSync(lockPath, `${process.pid}\n${Date.now()}`, { flag: "wx" });
-                hasLock = true;
-                break;
-            }
-            catch (err) {
-                if ((process.env.PHREN_DEBUG))
-                    process.stderr.write(`[phren] appendAuditLog lockWrite: ${errorMessage(err)}\n`);
-                try {
-                    const stat = fs.statSync(lockPath);
-                    if (Date.now() - stat.mtimeMs > staleMs) {
-                        try {
-                            fs.unlinkSync(lockPath);
-                        }
-                        catch {
-                            // Another process may have claimed or removed the stale lock between
-                            // statSync and unlinkSync. Sleep before retrying to avoid a spin loop.
-                            Atomics.wait(waiter, 0, 0, pollMs);
-                            waited += pollMs;
-                        }
-                        continue;
-                    }
-                }
-                catch (statErr) {
-                    if ((process.env.PHREN_DEBUG))
-                        process.stderr.write(`[phren] appendAuditLog staleStat: ${errorMessage(statErr)}\n`);
-                }
-                Atomics.wait(waiter, 0, 0, pollMs);
-                waited += pollMs;
-            }
-        }
-        if (hasLock) {
+        fs.mkdirSync(path.dirname(logPath), { recursive: true });
+        withFileLock(logPath, () => {
             fs.appendFileSync(logPath, line);
             const stat = fs.statSync(logPath);
             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");
             }
-        }
-        else {
-            debugLog(`Audit log skipped (lock timeout): ${event} ${details}`);
-        }
+        });
     }
     catch (err) {
         debugLog(`Audit log write failed: ${errorMessage(err)}`);
     }
-    finally {
-        if (hasLock) {
-            try {
-                fs.unlinkSync(lockPath);
-            }
-            catch (err) {
-                if ((process.env.PHREN_DEBUG))
-                    process.stderr.write(`[phren] appendAuditLog unlock: ${errorMessage(err)}\n`);
-            }
-        }
-    }
 }

package/mcp/dist/{shell-entry.js → shell/entry.js}

@@ -3,12 +3,12 @@
  * Extracted from shell.ts to keep the orchestrator under 300 lines.
  */
 import { PhrenShell } from "./shell.js";
-import { style, clearScreen, clearToEnd, shellStartupFrames, gradient, badge } from "./shell-render.js";
-import { createPhrenAnimator } from "./phren-art.js";
-import { errorMessage } from "./utils.js";
-import { computePhrenLiveStateToken } from "./shared.js";
-import { VERSION } from "./init-shared.js";
-import { loadShellState, saveShellState } from "./shell-state-store.js";
+import { style, clearScreen, clearToEnd, shellStartupFrames, gradient, badge } from "./render.js";
+import { createPhrenAnimator } from "../phren-art.js";
+import { errorMessage } from "../utils.js";
+import { computePhrenLiveStateToken } from "../shared.js";
+import { VERSION } from "../init/shared.js";
+import { loadShellState, saveShellState } from "./state-store.js";
 const LIVE_STATE_POLL_MS = 2000;
 function renderIntroFrame(frame, footer) {
     clearScreen();

package/mcp/dist/{shell-input.js → shell/input.js}

@@ -5,17 +5,18 @@
 import { execFileSync } from "child_process";
 import * as fs from "fs";
 import * as path from "path";
-import { addTask, addFinding, addProjectToProfile, completeTask, listProjectCards, pinTask, readTasks, readFindings, readReviewQueue, removeFinding, removeProjectFromProfile, resetShellState, saveShellState, setMachineProfile, tidyDoneTasks, canonicalTaskFilePath, unpinTask, updateTask, workNextTask, loadShellState, resolveTaskFilePath, } from "./data-access.js";
-import { runtimeFile } from "./shared.js";
-import { handleGovernMemories } from "./cli-govern.js";
-import { runSearch } from "./cli-search.js";
-import { consolidateProjectFindings } from "./governance-policy.js";
-import { style } from "./shell-render.js";
-import { SUB_VIEWS, TAB_ICONS } from "./shell-types.js";
-import { getProjectSkills, getHookEntries, writeInstallPreferences } from "./shell-view.js";
-import { removeSkillPath, setSkillEnabledAndSync } from "./skill-files.js";
-import { resultMsg, editDistance, tokenize, expandIds, normalizeSection, tasksByFilter, queueByFilter, } from "./shell-palette.js";
-import { errorMessage } from "./utils.js";
+import { addTask, addFinding, addProjectToProfile, completeTask, listProjectCards, pinTask, readTasks, readFindings, readReviewQueue, removeFinding, removeProjectFromProfile, resetShellState, saveShellState, setMachineProfile, tidyDoneTasks, canonicalTaskFilePath, unpinTask, updateTask, workNextTask, loadShellState, resolveTaskFilePath, } from "../data/access.js";
+import { runtimeFile } from "../shared.js";
+import { handleGovernMemories } from "../cli/govern.js";
+import { runSearch } from "../cli/search.js";
+import { consolidateProjectFindings } from "../governance/policy.js";
+import { style } from "./render.js";
+import { SUB_VIEWS, TAB_ICONS } from "./types.js";
+import { getProjectSkills, getHookEntries, writeInstallPreferences } from "./view.js";
+import { removeSkillPath, setSkillEnabledAndSync } from "../skill/files.js";
+import { resultMsg, editDistance, tokenize, expandIds, normalizeSection, tasksByFilter, queueByFilter, } from "./palette.js";
+import { errorMessage } from "../utils.js";
+import { logger } from "../logger.js";
 function taskFileForProject(phrenPath, project) {
     return resolveTaskFilePath(phrenPath, project)
         ?? canonicalTaskFilePath(phrenPath, project)
@@ -379,8 +380,7 @@ export async function executePalette(host, input) {
                 }
             }
             catch (err) {
-                if ((process.env.PHREN_DEBUG))
-                    process.stderr.write(`[phren] shell status gitStatus: ${errorMessage(err)}\n`);
+                logger.debug("shell-input", `shell status gitStatus: ${errorMessage(err)}`);
             }
             const auditPathNew = runtimeFile(host.phrenPath, "audit.log");
             const auditPathLegacy = path.join(host.phrenPath, ".config", "audit.log");

package/mcp/dist/{shell-palette.js → shell/palette.js}

@@ -1,9 +1,9 @@
 import { execFileSync } from "child_process";
 import * as path from "path";
 import { fileURLToPath } from "url";
-import { runLink } from "./link.js";
-import { runPhrenUpdate } from "./update.js";
-import { EXEC_TIMEOUT_MS, } from "./shared.js";
+import { runLink } from "../link/link.js";
+import { runPhrenUpdate } from "../update.js";
+import { EXEC_TIMEOUT_MS, } from "../shared.js";
 export function resultMsg(r) {
     if (!r.ok)
         return r.error;

package/mcp/dist/{shell-render.js → 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) {
@@ -150,7 +150,7 @@ const PHREN_LOGO = [
     "██║     ██║  ██║██║  ██║███████╗██║ ╚████║",
     "╚═╝     ╚═╝  ╚═╝╚═╝  ╚═╝╚══════╝╚═╝  ╚═══╝",
 ];
-import { PHREN_ART as PHREN_STARTUP_ART } from "./phren-art.js";
+import { PHREN_ART as PHREN_STARTUP_ART } from "../phren-art.js";
 // ── Line-based viewport: edge-triggered scroll (stable, no jumpiness) ─────────
 export function lineViewport(allLines, cursorFirstLine, cursorLastLine, height, prevStart) {
     if (allLines.length === 0 || height <= 0)

package/mcp/dist/{shell.js → shell/shell.js}

@@ -1,13 +1,14 @@
 import * as fs from "fs";
 import * as path from "path";
-import { addTask, addFinding, loadShellState, saveShellState, } from "./data-access.js";
-import { style } from "./shell-render.js";
-import { MAX_UNDO_STACK, } from "./shell-types.js";
-import { resultMsg, defaultRunHooks, defaultRunUpdate, defaultRunRelink, } from "./shell-palette.js";
-import { runDoctor } from "./link.js";
-import { renderShell, } from "./shell-view.js";
-import { executePalette, completeInput as completeInputFn, getListItems, handleNavigateKey, applyViewShortcut, } from "./shell-input.js";
-import { errorMessage } from "./utils.js";
+import { addTask, addFinding, loadShellState, saveShellState, } from "../data/access.js";
+import { style } from "./render.js";
+import { MAX_UNDO_STACK, } from "./types.js";
+import { logger } from "../logger.js";
+import { resultMsg, defaultRunHooks, defaultRunUpdate, defaultRunRelink, } from "./palette.js";
+import { runDoctor } from "../link/link.js";
+import { renderShell, } from "./view.js";
+import { executePalette, completeInput as completeInputFn, getListItems, handleNavigateKey, applyViewShortcut, } from "./input.js";
+import { errorMessage } from "../utils.js";
 // ── Shell class ──────────────────────────────────────────────────────────────
 export class PhrenShell {
     phrenPath;
@@ -72,8 +73,7 @@ export class PhrenShell {
             }
         }
         catch (err) {
-            if ((process.env.PHREN_DEBUG))
-                process.stderr.write(`[phren] shell pushUndo: ${errorMessage(err)}\n`);
+            logger.debug("shell", `shell pushUndo: ${errorMessage(err)}`);
         }
     }
     popUndo() {
@@ -294,4 +294,4 @@ export class PhrenShell {
         return completeInputFn(line, this.phrenPath, this.profile, this.state);
     }
 }
-export { startShell } from "./shell-entry.js";
+export { startShell } from "./entry.js";

package/mcp/dist/{shell-state-store.js → shell/state-store.js}

@@ -1,8 +1,9 @@
 import * as fs from "fs";
 import * as path from "path";
-import { phrenOk, shellStateFile } from "./shared.js";
-import { withSafeLock } from "./shared-data-utils.js";
-import { errorMessage } from "./utils.js";
+import { phrenOk, shellStateFile } from "../shared.js";
+import { withSafeLock } from "../shared/data-utils.js";
+import { errorMessage } from "../utils.js";
+import { logger } from "../logger.js";
 const SHELL_STATE_VERSION = 3;
 const VALID_VIEWS = new Set(["Projects", "Tasks", "Findings", "Review Queue", "Skills", "Hooks", "Machines/Profiles", "Health"]);
 export function loadShellState(phrenPath) {
@@ -33,8 +34,7 @@ export function loadShellState(phrenPath) {
         };
     }
     catch (err) {
-        if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] loadShellState parse: ${errorMessage(err)}\n`);
+        logger.debug("shell-state", `loadShellState parse: ${errorMessage(err)}`);
         return fallback;
     }
 }

package/mcp/dist/{shell-view-list.js → shell/view-list.js}

@@ -1,4 +1,4 @@
-import { RESET, padToWidth, truncateLine, lineViewport, style } from "./shell-render.js";
+import { RESET, padToWidth, truncateLine, lineViewport, style } from "./render.js";
 export function formatSelectableLine(line, cols, selected) {
     return selected
         ? `\x1b[7m${padToWidth(line, cols)}${RESET}`