@phren/cli 0.0.28 → 0.0.32

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";
@@ -123,8 +124,10 @@ 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 +184,7 @@ 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 +212,7 @@ 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 +249,7 @@ 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 +259,7 @@ 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 +304,7 @@ 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 +355,7 @@ 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 +2,7 @@ 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";
 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";
@@ -30,51 +31,9 @@ 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) {
@@ -82,23 +41,9 @@ export function appendAuditLog(phrenPath, event, details) {
                 const lines = content.split("\n");
                 fs.writeFileSync(logPath, lines.slice(-500).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}

@@ -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}`

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

@@ -4,16 +4,17 @@
  */
 import * as fs from "fs";
 import * as path from "path";
-import { canonicalTaskFilePath, listProjectCards, readTasks, readFindings, readReviewQueue, readRuntimeHealth, resolveTaskFilePath, } from "./data-access.js";
-import { style, badge, separator, stripAnsi, truncateLine, renderWidth, wrapSegments, lineViewport, shellHelpText, gradient, } from "./shell-render.js";
-import { formatSelectableLine, viewportWithStatus, } from "./shell-view-list.js";
-import { SUB_VIEWS, TAB_ICONS, } from "./shell-types.js";
-import { tasksByFilter, queueByFilter, } from "./shell-palette.js";
-import { listMachines, listProfiles, } from "./data-access.js";
-import { readInstallPreferences } from "./init-preferences.js";
-import { isProjectHookEnabled, readProjectConfig } from "./project-config.js";
-import { getScopedSkills } from "./skill-registry.js";
-import { errorMessage } from "./utils.js";
+import { canonicalTaskFilePath, listProjectCards, readTasks, readFindings, readReviewQueue, readRuntimeHealth, resolveTaskFilePath, } from "../data/access.js";
+import { style, badge, separator, stripAnsi, truncateLine, renderWidth, wrapSegments, lineViewport, shellHelpText, gradient, } from "./render.js";
+import { formatSelectableLine, viewportWithStatus, } from "./view-list.js";
+import { SUB_VIEWS, TAB_ICONS, } from "./types.js";
+import { tasksByFilter, queueByFilter, } from "./palette.js";
+import { listMachines, listProfiles, } from "../data/access.js";
+import { readInstallPreferences } from "../init/preferences.js";
+import { isProjectHookEnabled, readProjectConfig } from "../project-config.js";
+import { getScopedSkills } from "../skill/registry.js";
+import { errorMessage } from "../utils.js";
+import { logger } from "../logger.js";
 // ── Tab bar ────────────────────────────────────────────────────────────────
 function renderTabBar(state) {
     const cols = renderWidth();
@@ -249,8 +250,7 @@ function parseSubsections(taskPath, project, cache) {
         }
     }
     catch (err) {
-        if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] buildSubsectionMap: ${errorMessage(err)}\n`);
+        logger.debug("shell-view", `buildSubsectionMap: ${errorMessage(err)}`);
     }
     const newCache = { project, map };
     return { map, cache: newCache };
@@ -564,7 +564,7 @@ function renderHooksView(ctx, cursor, height) {
     ctx.setScroll(vp.scrollStart);
     return vp.lines;
 }
-export { writeInstallPreferences } from "./init-preferences.js";
+export { writeInstallPreferences } from "../init/preferences.js";
 // ── Machines/Profiles view ─────────────────────────────────────────────────
 function renderMachinesView(phrenPath) {
     const machines = listMachines(phrenPath);

package/mcp/dist/{skill-files.js → skill/files.js}

@@ -1,11 +1,12 @@
 import * as fs from "fs";
 import * as path from "path";
-import { homePath } from "./shared.js";
-import { findProjectDir } from "./project-locator.js";
-import { buildSkillManifest } from "./skill-registry.js";
-import { setSkillEnabled } from "./skill-state.js";
-import { errorMessage } from "./utils.js";
-import { isManagedSymlink } from "./link-skills.js";
+import { homePath } from "../shared.js";
+import { findProjectDir } from "../project-locator.js";
+import { buildSkillManifest } from "./registry.js";
+import { setSkillEnabled } from "./state.js";
+import { errorMessage } from "../utils.js";
+import { isManagedSymlink } from "../link/skills.js";
+import { logger } from "../logger.js";
 function normalizeSkillRemovalTarget(skillPath) {
     if (!skillPath)
         return skillPath;
@@ -44,9 +45,8 @@ function removeManagedSkillLink(dest, managedRoot) {
         fs.unlinkSync(dest);
     }
     catch (err) {
-        if (err.code !== "ENOENT" && (process.env.PHREN_DEBUG)) {
-            process.stderr.write(`[phren] removeManagedSkillLink: ${errorMessage(err)}\n`);
-        }
+        if (err.code !== "ENOENT")
+            logger.debug("skill-files", `removeManagedSkillLink: ${errorMessage(err)}`);
     }
 }
 function writeSkillArtifacts(destDir, manifest) {

package/mcp/dist/{skill-registry.js → skill/registry.js}

@@ -1,9 +1,9 @@
 import * as fs from "fs";
 import * as path from "path";
-import { getProjectDirs } from "./shared.js";
-import { parseSkillFrontmatter } from "./link-skills.js";
-import { isSkillEnabled } from "./skill-state.js";
-import { safeProjectPath } from "./utils.js";
+import { getProjectDirs } from "../shared.js";
+import { parseSkillFrontmatter } from "../link/skills.js";
+import { isSkillEnabled } from "./state.js";
+import { safeProjectPath } from "../utils.js";
 function normalizeCommand(raw, fallbackName) {
     const value = typeof raw === "string" && raw.trim() ? raw.trim() : `/${fallbackName}`;
     return value.startsWith("/") ? value : `/${value}`;

package/mcp/dist/{skill-state.js → skill/state.js}

@@ -1,4 +1,4 @@
-import { readInstallPreferences, writeInstallPreferences } from "./init-preferences.js";
+import { readInstallPreferences, writeInstallPreferences } from "../init/preferences.js";
 function skillStateKey(scope, name) {
     return `${scope}:${name.replace(/\.md$/i, "").trim().toLowerCase()}`;
 }

package/mcp/dist/startup-embedding.js

@@ -1,10 +1,10 @@
 import { debugLog } from "./shared.js";
-import { decodeStringRow, queryRows } from "./shared-index.js";
+import { decodeStringRow, queryRows } from "./shared/index.js";
 import { errorMessage } from "./utils.js";
 /** Throttle delay between embedding requests in the background embed loop. */
 const BACKGROUND_EMBED_THROTTLE_MS = 50;
 async function loadWarmupDeps() {
-    const { checkOllamaAvailable, embedText, getEmbeddingModel, getOllamaUrl } = await import("./shared-ollama.js");
+    const { checkOllamaAvailable, embedText, getEmbeddingModel, getOllamaUrl } = await import("./shared/ollama.js");
     return {
         checkOllamaAvailable,
         embedText,

package/mcp/dist/status.js

@@ -2,15 +2,16 @@ import * as fs from "fs";
 import * as path from "path";
 import { fileURLToPath } from "url";
 import { findPhrenPath, getProjectDirs, EXEC_TIMEOUT_QUICK_MS, debugLog, isRecord, hookConfigPath, homeDir, readRootManifest, } from "./shared.js";
-import { buildIndex, detectProject, findFtsCacheForPath, listIndexedDocumentPaths, queryRows } from "./shared-index.js";
-import { mergeConfig, getWorkflowPolicy } from "./shared-governance.js";
-import { getMcpEnabledPreference, getHooksEnabledPreference } from "./init.js";
+import { buildIndex, detectProject, findFtsCacheForPath, listIndexedDocumentPaths, queryRows } from "./shared/index.js";
+import { mergeConfig, getWorkflowPolicy } from "./shared/governance.js";
+import { getMcpEnabledPreference, getHooksEnabledPreference } from "./init/init.js";
 import { getTelemetrySummary } from "./telemetry.js";
 import { runGit as runGitShared, errorMessage } from "./utils.js";
-import { readRuntimeHealth, resolveTaskFilePath } from "./data-access.js";
+import { logger } from "./logger.js";
+import { readRuntimeHealth, resolveTaskFilePath } from "./data/access.js";
 import { resolveRuntimeProfile } from "./runtime-profile.js";
 import { renderPhrenArt } from "./phren-art.js";
-import { RESET, BOLD, DIM, GREEN, YELLOW, RED, CYAN } from "./shell-render.js";
+import { RESET, BOLD, DIM, GREEN, YELLOW, RED, CYAN } from "./shell/render.js";
 const __dirname = path.dirname(fileURLToPath(import.meta.url));
 function readPackageVersion() {
     try {
@@ -20,7 +21,7 @@ function readPackageVersion() {
     }
     catch (err) {
         if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] readPackageVersion: ${errorMessage(err)}\n`);
+            logger.debug("status", `readPackageVersion: ${errorMessage(err)}`);
         return "unknown";
     }
 }
@@ -91,7 +92,7 @@ export async function runStatus() {
         }
         catch (err) {
             if ((process.env.PHREN_DEBUG))
-                process.stderr.write(`[phren] statusConfig: ${errorMessage(err)}\n`);
+                logger.debug("status", `statusConfig: ${errorMessage(err)}`);
         }
     }
     // Phren path and config
@@ -125,7 +126,7 @@ export async function runStatus() {
             }
             catch (err) {
                 if ((process.env.PHREN_DEBUG))
-                    process.stderr.write(`[phren] statusWorkspaceMcp parse: ${errorMessage(err)}\n`);
+                    logger.debug("status", `statusWorkspaceMcp parse: ${errorMessage(err)}`);
             }
         }
     }
@@ -143,7 +144,7 @@ export async function runStatus() {
             }
             catch (err) {
                 if ((process.env.PHREN_DEBUG))
-                    process.stderr.write(`[phren] statusHooks settingsParse: ${errorMessage(err)}\n`);
+                    logger.debug("status", `statusHooks settingsParse: ${errorMessage(err)}`);
             }
         }
     }
@@ -174,15 +175,15 @@ export async function runStatus() {
     }
     catch (err) {
         if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] statusFtsIndex: ${errorMessage(err)}\n`);
+            logger.debug("status", `statusFtsIndex: ${errorMessage(err)}`);
     }
     const ftsLabel = ftsIndexOk
         ? `${GREEN}ok${RESET} ${DIM}(${ftsIndexSize > 0 ? `${(ftsIndexSize / 1024).toFixed(0)} KB` : `${ftsDocCount ?? 0} docs`})${RESET}`
         : `${YELLOW}not built${RESET} ${DIM}(run a search to build)${RESET}`;
     console.log(`  ${DIM}fts${RESET}      ${ftsLabel}`);
     try {
-        const { getOllamaUrl, checkOllamaAvailable, checkModelAvailable, getEmbeddingModel } = await import("./shared-ollama.js");
-        const { getEmbeddingCache, formatEmbeddingCoverage } = await import("./shared-embedding-cache.js");
+        const { getOllamaUrl, checkOllamaAvailable, checkModelAvailable, getEmbeddingModel } = await import("./shared/ollama.js");
+        const { getEmbeddingCache, formatEmbeddingCoverage } = await import("./shared/embedding-cache.js");
         const ollamaUrl = getOllamaUrl();
         if (!ollamaUrl) {
             console.log(`  ${DIM}semantic${RESET} ${DIM}disabled (optional)${RESET}`);
@@ -209,7 +210,7 @@ export async function runStatus() {
     }
     catch (err) {
         if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] statusSemantic: ${errorMessage(err)}\n`);
+            logger.debug("status", `statusSemantic: ${errorMessage(err)}`);
     }
     // Agent integration status
     function hasPhrenEntry(filePath) {
@@ -221,7 +222,7 @@ export async function runStatus() {
         }
         catch (err) {
             if ((process.env.PHREN_DEBUG))
-                process.stderr.write(`[phren] hasPhrenEntry: ${errorMessage(err)}\n`);
+                logger.debug("status", `hasPhrenEntry: ${errorMessage(err)}`);
             return false;
         }
     }

package/mcp/dist/{tasks-github.js → task/github.js}

@@ -1,8 +1,8 @@
 import * as fs from "fs";
 import * as path from "path";
 import { execFileSync } from "child_process";
-import { EXEC_TIMEOUT_MS, phrenErr, phrenOk, PhrenError } from "./shared.js";
-import { errorMessage, resolveExecCommand } from "./utils.js";
+import { EXEC_TIMEOUT_MS, phrenErr, phrenOk, PhrenError } from "../shared.js";
+import { errorMessage, resolveExecCommand } from "../utils.js";
 const GITHUB_REPO_URL = /https:\/\/github\.com\/([A-Za-z0-9_.-]+\/[A-Za-z0-9_.-]+)(?:\/|\b|$)/;
 const GITHUB_ISSUE_URL = /https:\/\/github\.com\/([A-Za-z0-9_.-]+\/[A-Za-z0-9_.-]+)\/issues\/(\d+)(?:[?#][^\s]*)?$/;
 export function parseGithubIssueUrl(url) {

package/mcp/dist/{task-hygiene.js → task/hygiene.js}

@@ -1,7 +1,8 @@
 import * as fs from "fs";
 import * as path from "path";
-import { isTaskFileName, readTasks } from "./data-tasks.js";
-import { STOP_WORDS, extractKeywords, errorMessage } from "./utils.js";
+import { isTaskFileName, readTasks } from "../data/tasks.js";
+import { STOP_WORDS, extractKeywords, errorMessage } from "../utils.js";
+import { logger } from "../logger.js";
 const TEXT_EXTENSIONS = new Set([
     ".cjs",
     ".css",
@@ -141,8 +142,7 @@ function collectCorpus(root) {
                 texts.push(fs.readFileSync(fullPath, "utf8").slice(0, MAX_TEXT_BYTES).toLowerCase());
             }
             catch (err) {
-                if ((process.env.PHREN_DEBUG))
-                    process.stderr.write(`[phren] task hygiene read ${fullPath}: ${errorMessage(err)}\n`);
+                logger.debug("task-hygiene", `task hygiene read ${fullPath}: ${errorMessage(err)}`);
             }
             if (filesSeen >= MAX_FILES_PER_ROOT)
                 break;

package/mcp/dist/{task-lifecycle.js → task/lifecycle.js}

@@ -1,11 +1,11 @@
 import * as fs from "fs";
-import { addTask, completeTask, readTasks, resolveTaskItem, updateTask, } from "./data-access.js";
-import { parseGithubIssueUrl, resolveProjectGithubRepo } from "./tasks-github.js";
-import { getProactivityLevelForTask, shouldAutoCaptureTaskForLevel, hasExecutionIntent, hasDiscoveryIntent, hasSuppressTaskIntent, hasCodeChangeContext } from "./proactivity.js";
-import { getWorkflowPolicy } from "./shared-governance.js";
-import { debugLog, sessionMarker } from "./shared.js";
-import { errorMessage } from "./utils.js";
-import { incrementSessionTasksCompleted } from "./mcp-session.js";
+import { addTask, completeTask, readTasks, resolveTaskItem, updateTask, } from "../data/access.js";
+import { parseGithubIssueUrl, resolveProjectGithubRepo } from "./github.js";
+import { getProactivityLevelForTask, shouldAutoCaptureTaskForLevel, hasExecutionIntent, hasDiscoveryIntent, hasSuppressTaskIntent, hasCodeChangeContext } from "../proactivity.js";
+import { getWorkflowPolicy } from "../shared/governance.js";
+import { debugLog, sessionMarker } from "../shared.js";
+import { errorMessage } from "../utils.js";
+import { incrementSessionTasksCompleted } from "../tools/session.js";
 const ACTION_PREFIX_RE = /^(?:please\s+|can you\s+|could you\s+|would you\s+|i want you to\s+|i want to\s+|let(?:'|’)s\s+|lets\s+|help me\s+)/i;
 const EXPLICIT_TASK_PREFIX_RE = /^(?:add(?:\s+(?:this|that|it))?\s+(?:to\s+(?:the\s+)?)?(?:task|todo(?:\s+list)?|task(?:\s+list)?)|add\s+(?:a\s+)?task|put(?:\s+(?:this|that|it))?\s+(?:in|on)\s+(?:the\s+)?(?:task|todo(?:\s+list)?|task(?:\s+list)?))\s*(?::|-|,)?\s*/i;
 const NON_ACTIONABLE_RE = /\b(brainstorm|idea|ideas|maybe|what if|should we|could we|would it make sense|question|explain|why is|how does)\b/i;