@phren/cli 0.0.28 → 0.0.33

package/mcp/dist/proactivity.js

@@ -1,9 +1,9 @@
 import * as fs from "fs";
 import { bootstrapPhrenDotEnv } from "./phren-dotenv.js";
 import { debugLog, findPhrenPath } from "./phren-paths.js";
-import { governanceInstallPreferencesFile, readInstallPreferences } from "./init-preferences.js";
+import { governanceInstallPreferencesFile, readInstallPreferences } from "./init/preferences.js";
 import { errorMessage } from "./utils.js";
-import { getWorkflowPolicy } from "./governance-policy.js";
+import { getWorkflowPolicy } from "./governance/policy.js";
 export const PROACTIVITY_LEVELS = ["high", "medium", "low"];
 const DEFAULT_PROACTIVITY_LEVEL = "high";
 const EXPLICIT_FINDING_SIGNAL_PATTERN = /\b(add finding|worth remembering)\b/i;
@@ -21,7 +21,7 @@ function resolveProactivityPhrenPath(explicitPhrenPath) {
     return explicitPhrenPath ?? findPhrenPath();
 }
 /** Read per-user preferences from ~/.phren/.users/<actor>/preferences.json. Actor from PHREN_ACTOR env var. */
-export function readUserPreferences(explicitPhrenPath) {
+function readUserPreferences(explicitPhrenPath) {
     const phrenPath = resolveProactivityPhrenPath(explicitPhrenPath);
     if (!phrenPath)
         return {};

package/mcp/dist/profile-store.js

@@ -5,8 +5,9 @@ import * as yaml from "js-yaml";
 import { phrenErr, PhrenError, phrenOk, forwardErr, getProjectDirs, readRootManifest, } from "./shared.js";
 import { defaultMachineName, getMachineName } from "./machine-identity.js";
 import { errorMessage, isValidProjectName } from "./utils.js";
-import { TASK_FILE_ALIASES } from "./data-tasks.js";
-import { withSafeLock } from "./shared-data-utils.js";
+import { TASK_FILE_ALIASES } from "./data/tasks.js";
+import { withSafeLock } from "./shared/data-utils.js";
+import { logger } from "./logger.js";
 export function resolveActiveProfile(phrenPath, requestedProfile) {
     const manifest = readRootManifest(phrenPath);
     if (manifest?.installMode === "project-local") {
@@ -61,8 +62,7 @@ export function listMachines(phrenPath) {
         return phrenOk(cleaned);
     }
     catch (err) {
-        if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] listMachines yaml parse: ${errorMessage(err)}\n`);
+        logger.debug("profile-store", `listMachines yaml parse: ${errorMessage(err)}`);
         return phrenErr(`Could not parse machines.yaml. Check the file for syntax errors or run 'phren doctor --fix'.`, PhrenError.MALFORMED_YAML);
     }
 }
@@ -226,8 +226,7 @@ export function listProfiles(phrenPath) {
             profiles.push({ name, file: full, projects, ...(defaults ? { defaults } : {}) });
         }
         catch (err) {
-            if ((process.env.PHREN_DEBUG))
-                process.stderr.write(`[phren] listProfiles yamlParse: ${errorMessage(err)}\n`);
+            logger.debug("profile-store", `listProfiles yamlParse: ${errorMessage(err)}`);
             return phrenErr(`profiles/${file}`, PhrenError.MALFORMED_YAML);
         }
     }

package/mcp/dist/project-config.js

@@ -2,10 +2,10 @@ import * as crypto from "crypto";
 import * as fs from "fs";
 import * as path from "path";
 import * as yaml from "js-yaml";
-import { readInstallPreferences } from "./init-preferences.js";
+import { readInstallPreferences } from "./init/preferences.js";
 import { debugLog } from "./shared.js";
 import { errorMessage, safeProjectPath } from "./utils.js";
-import { withFileLock } from "./shared-governance.js";
+import { withFileLock } from "./shared/governance.js";
 export const PROJECT_OWNERSHIP_MODES = ["phren-managed", "detached", "repo-managed"];
 export const PROJECT_HOOK_EVENTS = ["UserPromptSubmit", "Stop", "SessionStart", "PostToolUse"];
 export function parseProjectOwnershipMode(raw) {

package/mcp/dist/project-topics.js

@@ -2,8 +2,9 @@ import * as crypto from "crypto";
 import * as fs from "fs";
 import * as path from "path";
 import { debugLog } from "./shared.js";
-import { withFileLock } from "./shared-governance.js";
+import { withFileLock } from "./shared/governance.js";
 import { STOP_WORDS, errorMessage, extractKeywords, isValidProjectName, safeProjectPath } from "./utils.js";
+import { walkDirectory } from "./shared/data-utils.js";
 const TOPIC_CONFIG_FILENAME = "topic-config.json";
 const AUTO_TOPIC_MARKER_RE = /^<!--\s*phren:auto-topic(?:\s+slug=([a-z0-9_-]+))?\s*-->$/;
 const ARCHIVED_SECTION_RE = /^## Archived (\d{4}-\d{2}-\d{2})$/;
@@ -303,7 +304,7 @@ function normalizeKeyword(raw) {
         .replace(/\s+/g, " ")
         .trim();
 }
-export function normalizeTopicSlug(raw) {
+function normalizeTopicSlug(raw) {
     return raw
         .trim()
         .toLowerCase()
@@ -384,10 +385,7 @@ function topicConfigPath(phrenPath, project) {
 function projectDirPath(phrenPath, project) {
     return safeProjectPath(phrenPath, project);
 }
-export function topicReferenceDir(phrenPath, project) {
-    return safeProjectPath(phrenPath, project, "reference", "topics");
-}
-export function topicReferenceRelativePath(slug) {
+function topicReferenceRelativePath(slug) {
     return path.posix.join("reference", "topics", `${slug}.md`);
 }
 export function topicReferencePath(phrenPath, project, slug) {
@@ -575,7 +573,7 @@ export function readProjectTopics(phrenPath, project) {
     }
     return { source: "custom", topics: normalized, domain: typeof parsed.domain === "string" ? parsed.domain : undefined };
 }
-export function readPinnedTopics(phrenPath, project) {
+function readPinnedTopics(phrenPath, project) {
     const configPath = topicConfigPath(phrenPath, project);
     if (!configPath || !fs.existsSync(configPath))
         return [];
@@ -675,27 +673,14 @@ function normalizeBullet(line) {
 }
 function collectArchivedBulletsRecursively(dirPath) {
     const bullets = new Set();
-    if (!fs.existsSync(dirPath))
-        return bullets;
-    const stack = [dirPath];
-    while (stack.length > 0) {
-        const current = stack.pop();
-        for (const entry of fs.readdirSync(current, { withFileTypes: true })) {
-            const fullPath = path.join(current, entry.name);
-            if (entry.isDirectory()) {
-                stack.push(fullPath);
-                continue;
-            }
-            if (!entry.isFile() || !entry.name.endsWith(".md"))
+    for (const filePath of walkDirectory(dirPath)) {
+        const content = fs.readFileSync(filePath, "utf8");
+        for (const line of content.split("\n")) {
+            if (!line.startsWith("- "))
                 continue;
-            const content = fs.readFileSync(fullPath, "utf8");
-            for (const line of content.split("\n")) {
-                if (!line.startsWith("- "))
-                    continue;
-                const normalized = normalizeBullet(line);
-                if (normalized)
-                    bullets.add(normalized);
-            }
+            const normalized = normalizeBullet(line);
+            if (normalized)
+                bullets.add(normalized);
         }
     }
     return bullets;
@@ -797,23 +782,7 @@ function parseLegacyTopicEntries(content, project) {
     return { slug: fallbackSlug, entries };
 }
 function readReferenceMarkdownFiles(referenceDir) {
-    if (!fs.existsSync(referenceDir))
-        return [];
-    const files = [];
-    const stack = [referenceDir];
-    while (stack.length > 0) {
-        const current = stack.pop();
-        for (const entry of fs.readdirSync(current, { withFileTypes: true })) {
-            const fullPath = path.join(current, entry.name);
-            if (entry.isDirectory()) {
-                stack.push(fullPath);
-                continue;
-            }
-            if (entry.isFile() && entry.name.endsWith(".md"))
-                files.push(fullPath);
-        }
-    }
-    return files.sort();
+    return walkDirectory(referenceDir).sort();
 }
 function relativeToProject(projectDir, filePath) {
     return path.relative(projectDir, filePath).replace(/\\/g, "/");
@@ -835,7 +804,7 @@ function safeStatIso(filePath) {
         return "";
     }
 }
-export function listProjectTopicDocs(phrenPath, project, topics) {
+function listProjectTopicDocs(phrenPath, project, topics) {
     const projectDir = projectDirPath(phrenPath, project);
     if (!projectDir)
         return [];
@@ -885,7 +854,7 @@ export function listProjectReferenceDocs(phrenPath, project, topics) {
     }
     return { topicDocs, otherDocs };
 }
-export function listLegacyTopicDocs(phrenPath, project) {
+function listLegacyTopicDocs(phrenPath, project) {
     const projectDir = projectDirPath(phrenPath, project);
     const referenceDir = safeProjectPath(phrenPath, project, "reference");
     if (!projectDir || !referenceDir || !fs.existsSync(referenceDir))
@@ -1042,6 +1011,7 @@ export function suggestTopics(phrenPath, project, topics) {
     }
     return deduped;
 }
+/** @internal Exported for tests. */
 export const suggestProjectTopics = suggestTopics;
 export function getProjectTopicsResponse(phrenPath, project) {
     const { source, topics } = readProjectTopics(phrenPath, project);
@@ -1054,7 +1024,7 @@ export function getProjectTopicsResponse(phrenPath, project) {
         topicDocs: listProjectTopicDocs(phrenPath, project, topics),
     };
 }
-export function resolveReferenceContentPath(phrenPath, project, file) {
+function resolveReferenceContentPath(phrenPath, project, file) {
     if (!isValidProjectName(project) || !file || file.includes("\0"))
         return null;
     if (!file.endsWith(".md"))

package/mcp/dist/provider-adapters.js

@@ -35,7 +35,7 @@ function normalizeWindowsPathToWsl(input) {
 function uniqStrings(values) {
     return Array.from(new Set(values.filter((value) => Boolean(value && value.trim()))));
 }
-export function pickExistingFile(candidates) {
+function pickExistingFile(candidates) {
     for (const candidate of candidates) {
         if (fs.existsSync(candidate))
             return candidate;

package/mcp/dist/query-correlation.js

@@ -7,7 +7,7 @@
 import * as fs from "fs";
 import { runtimeFile, debugLog } from "./shared.js";
 import { isFeatureEnabled, errorMessage } from "./utils.js";
-import { withFileLock } from "./shared-governance.js";
+import { withFileLock } from "./shared/governance.js";
 const CORRELATION_FILENAME = "query-correlations.jsonl";
 const RECENT_WINDOW = 500;
 const MIN_TOKEN_OVERLAP = 2;

package/mcp/dist/runtime-profile.js

@@ -1,5 +1,5 @@
 import { resolveActiveProfile } from "./profile-store.js";
-export function requestedProfileFromEnv() {
+function requestedProfileFromEnv() {
     const profile = (process.env.PHREN_PROFILE)?.trim();
     return profile ? profile : undefined;
 }

package/mcp/dist/{session-checkpoints.js → session/checkpoints.js}

@@ -1,8 +1,8 @@
 import * as fs from "fs";
 import * as path from "path";
-import { errorMessage } from "./utils.js";
-import { debugLog, sessionMarker } from "./shared.js";
-import { atomicWriteJson } from "./session-utils.js";
+import { errorMessage } from "../utils.js";
+import { debugLog, sessionMarker } from "../shared.js";
+import { atomicWriteJson } from "./utils.js";
 function sanitizeFileSegment(value) {
     const trimmed = value.trim();
     const safe = trimmed.replace(/[^a-zA-Z0-9._-]+/g, "_");

package/mcp/dist/{session-utils.js → session/utils.js}

@@ -1,6 +1,6 @@
 import * as fs from "fs";
 import * as path from "path";
-import { errorMessage } from "./utils.js";
+import { errorMessage } from "../utils.js";
 /**
  * Write JSON to a file atomically using temp-file + rename.
  * Ensures the parent directory exists before writing.

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

@@ -1,8 +1,8 @@
 // Barrel re-export. Internal code imports from the specific modules directly.
-export { checkConsolidationNeeded, validateFindingsFormat, stripTaskDoneSection, validateTaskFormat, extractConflictVersions, mergeFindings, mergeTask, autoMergeConflicts, } from "./content-validate.js";
-export { filterTrustedFindings, filterTrustedFindingsDetailed, } from "./content-citation.js";
-export { scanForSecrets, resolveCoref, isDuplicateFinding, detectConflicts, extractDynamicEntities, checkSemanticDedup, checkSemanticConflicts, } from "./content-dedup.js";
-export { countActiveFindings, autoArchiveToReference, } from "./content-archive.js";
-export { upsertCanonical, addFindingToFile, addFindingsToFile, autoDetectFindingType, } from "./content-learning.js";
-export { FINDING_LIFECYCLE_STATUSES, FINDING_TYPE_DECAY, extractFindingType, parseFindingLifecycle, buildLifecycleComments, isInactiveFindingLine, } from "./finding-lifecycle.js";
-export { METADATA_REGEX, parseStatus, parseStatusField, parseSupersession, parseSupersedesRef, parseContradiction, parseAllContradictions, parseFindingId, parseCreatedDate, isCitationLine, isArchiveStart, isArchiveEnd, stripLifecycleMetadata, stripRelationMetadata, stripAllMetadata, stripComments, addMetadata, } from "./content-metadata.js";
+export { checkConsolidationNeeded, validateFindingsFormat, stripTaskDoneSection, validateTaskFormat, extractConflictVersions, mergeFindings, mergeTask, autoMergeConflicts, } from "../content/validate.js";
+export { filterTrustedFindings, filterTrustedFindingsDetailed, } from "../content/citation.js";
+export { scanForSecrets, resolveCoref, isDuplicateFinding, detectConflicts, extractDynamicEntities, checkSemanticDedup, checkSemanticConflicts, } from "../content/dedup.js";
+export { countActiveFindings, autoArchiveToReference, } from "../content/archive.js";
+export { upsertCanonical, addFindingToFile, addFindingsToFile, autoDetectFindingType, } from "../content/learning.js";
+export { FINDING_LIFECYCLE_STATUSES, FINDING_TYPE_DECAY, extractFindingType, parseFindingLifecycle, buildLifecycleComments, isInactiveFindingLine, } from "../finding/lifecycle.js";
+export { METADATA_REGEX, parseStatus, parseStatusField, parseSupersession, parseSupersedesRef, parseContradiction, parseAllContradictions, parseFindingId, parseCreatedDate, isCitationLine, isArchiveStart, isArchiveEnd, stripLifecycleMetadata, stripRelationMetadata, stripAllMetadata, stripComments, addMetadata, } from "../content/metadata.js";

package/mcp/dist/{shared-data-utils.js → shared/data-utils.js}

@@ -1,8 +1,8 @@
 import * as fs from "fs";
 import * as path from "path";
-import { phrenErr, PhrenError, phrenOk, } from "./shared.js";
-import { withFileLock as withFileLockRaw } from "./shared-governance.js";
-import { isValidProjectName, safeProjectPath, errorMessage } from "./utils.js";
+import { phrenErr, PhrenError, phrenOk, } from "../shared.js";
+import { withFileLock as withFileLockRaw } from "./governance.js";
+import { isValidProjectName, safeProjectPath, errorMessage } from "../utils.js";
 export function withSafeLock(filePath, fn) {
     try {
         return withFileLockRaw(filePath, fn);
@@ -15,6 +15,31 @@ export function withSafeLock(filePath, fn) {
         throw err;
     }
 }
+/**
+ * Recursively walk a directory and return paths of files matching an optional filter.
+ * Defaults to `.md` files only. Uses an iterative stack to avoid recursion limits.
+ */
+export function walkDirectory(root, filter) {
+    const accept = filter ?? ((name) => name.endsWith(".md"));
+    const results = [];
+    if (!fs.existsSync(root))
+        return results;
+    const stack = [root];
+    while (stack.length > 0) {
+        const current = stack.pop();
+        for (const entry of fs.readdirSync(current, { withFileTypes: true })) {
+            const fullPath = path.join(current, entry.name);
+            if (entry.isDirectory()) {
+                stack.push(fullPath);
+                continue;
+            }
+            if (entry.isFile() && accept(entry.name)) {
+                results.push(fullPath);
+            }
+        }
+    }
+    return results;
+}
 export function ensureProject(phrenPath, project) {
     if (!isValidProjectName(project))
         return phrenErr(`Project name "${project}" is not valid. Use lowercase letters, numbers, and hyphens (e.g. "my-project").`, PhrenError.INVALID_PROJECT_NAME);

package/mcp/dist/{shared-embedding-cache.js → shared/embedding-cache.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";
 function isEmbeddingEntry(value) {
     if (!value || typeof value !== "object" || Array.isArray(value))
         return false;

package/mcp/dist/{shared-fragment-graph.js → shared/fragment-graph.js}

@@ -1,10 +1,13 @@
-import { decodeStringRow } from "./shared-index.js";
+import { decodeStringRow } from "./index.js";
 import * as fs from "fs";
-import { runtimeFile } from "./shared.js";
-import { UNIVERSAL_TECH_TERMS_RE } from "./phren-core.js";
-import { errorMessage } from "./utils.js";
+import { runtimeFile } from "../shared.js";
+import { logger } from "../logger.js";
+import { UNIVERSAL_TECH_TERMS_RE } from "../phren-core.js";
+import { errorMessage } from "../utils.js";
+/** @internal Exported for tests. */
 export function escapeRegex(s) { return s.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); }
-/** Escape SQL LIKE wildcard characters so user input is treated literally. */
+/** Escape SQL LIKE wildcard characters so user input is treated literally.
+ * @internal Exported for tests. */
 export function escapeLike(s) { return s.replace(/[%_\\]/g, '\\$&'); }
 /**
  * Log fragment resolution misses to .runtime/fragment-misses.jsonl.
@@ -40,8 +43,6 @@ export function logFragmentMiss(phrenPath, name, context, project) {
         // Best-effort logging; don't let miss tracking break the caller.
     }
 }
-/** @deprecated Use logFragmentMiss instead */
-export const logEntityMiss = logFragmentMiss;
 // Use the shared universal starter set. Framework/tool specifics are learned
 // dynamically per project via extractDynamicFragments() in content-dedup.ts.
 const PROSE_FRAGMENT_PATTERN = UNIVERSAL_TECH_TERMS_RE;
@@ -109,15 +110,12 @@ export function extractFragmentNames(content) {
     }
     return [...found];
 }
-/** @deprecated Use extractFragmentNames instead */
-export const extractEntityNames = extractFragmentNames;
 function getOrCreateFragment(db, name, type) {
     try {
         db.run("INSERT OR IGNORE INTO entities (name, type, first_seen_at) VALUES (?, ?, ?)", [name, type, new Date().toISOString().slice(0, 10)]);
     }
     catch (err) {
-        if (process.env.PHREN_DEBUG)
-            process.stderr.write(`[phren] fragmentInsert: ${errorMessage(err)}\n`);
+        logger.debug("fragmentInsert", errorMessage(err));
     }
     const result = db.exec("SELECT id FROM entities WHERE name = ? AND type = ?", [name, type]);
     if (result?.length && result[0]?.values?.length) {
@@ -139,8 +137,7 @@ export function ensureGlobalEntitiesTable(db) {
       )`);
     }
     catch (err) {
-        if (process.env.PHREN_DEBUG)
-            process.stderr.write(`[phren] ensureGlobalEntitiesTable: ${errorMessage(err)}\n`);
+        logger.debug("ensureGlobalEntitiesTable", errorMessage(err));
     }
 }
 /**
@@ -186,14 +183,11 @@ export function beginUserFragmentBuildCache(phrenPath, projects) {
             _buildUserFragmentCache.set(cacheKey, loaded.fragments);
         }
         catch (err) {
-            if (process.env.PHREN_DEBUG)
-                process.stderr.write(`[phren] beginUserFragmentBuildCache: ${errorMessage(err)}\n`);
+            logger.debug("beginUserFragmentBuildCache", errorMessage(err));
             _buildUserFragmentCache.set(cacheKey, []);
         }
     }
 }
-/** @deprecated Use beginUserFragmentBuildCache instead */
-export const beginUserEntityBuildCache = beginUserFragmentBuildCache;
 /** End a build-scoped cache created by beginUserFragmentBuildCache(). */
 export function endUserFragmentBuildCache(phrenPath) {
     const prefix = `${phrenPath}/`;
@@ -204,8 +198,6 @@ export function endUserFragmentBuildCache(phrenPath) {
     if (_activeBuildCacheKeyPrefix === prefix)
         _activeBuildCacheKeyPrefix = null;
 }
-/** @deprecated Use endUserFragmentBuildCache instead */
-export const endUserEntityBuildCache = endUserFragmentBuildCache;
 function parseUserDefinedFragments(phrenPath, project) {
     const claudeMdPath = `${phrenPath}/${project}/CLAUDE.md`;
     const cacheKey = `${phrenPath}/${project}`;
@@ -225,8 +217,7 @@ function parseUserDefinedFragments(phrenPath, project) {
                 }
             }
             catch (err) {
-                if (process.env.PHREN_DEBUG)
-                    process.stderr.write(`[phren] parseUserDefinedFragments statCheck: ${errorMessage(err)}\n`);
+                logger.debug("parseUserDefinedFragments statCheck", errorMessage(err));
             }
         }
         const loaded = readUserDefinedFragmentsFromDisk(claudeMdPath);
@@ -236,19 +227,16 @@ function parseUserDefinedFragments(phrenPath, project) {
         return loaded.fragments;
     }
     catch (err) {
-        if (process.env.PHREN_DEBUG)
-            process.stderr.write(`[phren] parseUserDefinedFragments: ${errorMessage(err)}\n`);
+        logger.debug("parseUserDefinedFragments", errorMessage(err));
         return [];
     }
 }
 /** Clear the user fragment cache (call between index builds). */
-export function clearUserFragmentCache() {
+function clearUserFragmentCache() {
     _userFragmentCache.clear();
     _buildUserFragmentCache.clear();
     _activeBuildCacheKeyPrefix = null;
 }
-/** @deprecated Use clearUserFragmentCache instead */
-export const clearUserEntityCache = clearUserFragmentCache;
 // Words that commonly start sentences or appear in titles — not fragment names
 const SENTENCE_START_WORDS = new Set([
     "the", "this", "that", "these", "those", "when", "where", "which", "while",
@@ -353,8 +341,7 @@ export function extractAndLinkFragments(db, content, sourceDoc, phrenPath) {
             db.run("INSERT OR IGNORE INTO entity_links (source_id, target_id, rel_type, source_doc) VALUES (?, ?, ?, ?)", [docFragmentId, fragmentId, "mentions", sourceDoc]);
         }
         catch (err) {
-            if (process.env.PHREN_DEBUG)
-                process.stderr.write(`[phren] fragmentLinksInsert: ${errorMessage(err)}\n`);
+            logger.debug("fragmentLinksInsert", errorMessage(err));
         }
         // Write to global_entities for cross-project queries
         if (project) {
@@ -362,14 +349,11 @@ export function extractAndLinkFragments(db, content, sourceDoc, phrenPath) {
                 db.run("INSERT OR IGNORE INTO global_entities (entity, project, doc_key) VALUES (?, ?, ?)", [name, project, sourceDoc]);
             }
             catch (err) {
-                if (process.env.PHREN_DEBUG)
-                    process.stderr.write(`[phren] globalFragmentsInsert: ${errorMessage(err)}\n`);
+                logger.debug("globalFragmentsInsert", errorMessage(err));
             }
         }
     }
 }
-/** @deprecated Use extractAndLinkFragments instead */
-export const extractAndLinkEntities = extractAndLinkFragments;
 /**
  * Query related fragments for a given name.
  */
@@ -391,13 +375,10 @@ export function queryFragmentLinks(db, name) {
         }
     }
     catch (err) {
-        if (process.env.PHREN_DEBUG)
-            process.stderr.write(`[phren] queryFragmentLinks: ${errorMessage(err)}\n`);
+        logger.debug("queryFragmentLinks", errorMessage(err));
     }
     return { related };
 }
-/** @deprecated Use queryFragmentLinks instead */
-export const queryEntityLinks = queryFragmentLinks;
 /**
  * Query cross-project fragment relationships.
  * Returns projects and docs that share fragments with the given query.
@@ -427,8 +408,7 @@ export function queryCrossProjectFragments(db, fragmentName, excludeProject) {
         }
     }
     catch (err) {
-        if (process.env.PHREN_DEBUG)
-            process.stderr.write(`[phren] queryCrossProjectFragments: ${errorMessage(err)}\n`);
+        logger.debug("queryCrossProjectFragments", errorMessage(err));
     }
     return results;
 }
@@ -448,10 +428,7 @@ export function getFragmentBoostDocs(db, query) {
         return boostDocs;
     }
     catch (err) {
-        if (process.env.PHREN_DEBUG)
-            process.stderr.write(`[phren] getFragmentBoostDocs: ${errorMessage(err)}\n`);
+        logger.debug("getFragmentBoostDocs", errorMessage(err));
         return new Set();
     }
 }
-/** @deprecated Use getFragmentBoostDocs instead */
-export const getEntityBoostDocs = getFragmentBoostDocs;

package/mcp/dist/shared/governance.js

@@ -0,0 +1,4 @@
+export * from '../governance/policy.js';
+export * from '../governance/scores.js';
+export * from '../governance/audit.js';
+export { withFileLock, isFiniteNumber, hasValidSchemaVersion } from '../governance/locks.js';