@phren/cli 0.0.28 → 0.0.32

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

@@ -3,27 +3,28 @@ import * as path from "path";
 import * as readline from "readline";
 import * as yaml from "js-yaml";
 import { execFileSync } from "child_process";
-import { ROOT } from "./package-metadata.js";
-import { configureMcpTargets, ensureGovernanceFiles, getHooksEnabledPreference, getMcpEnabledPreference, isVersionNewer, patchJsonFile, setMcpEnabledPreference, } from "./init.js";
-import { configureAllHooks, detectInstalledTools } from "./hooks.js";
-import { getMachineName, persistMachineName } from "./machine-identity.js";
-import { debugLog, EXEC_TIMEOUT_MS, EXEC_TIMEOUT_QUICK_MS, isRecord, homePath, hookConfigPath, installPreferencesFile, atomicWriteText, } from "./shared.js";
-import { errorMessage } from "./utils.js";
-import { log } from "./init-shared.js";
-import { listMachines as listMachinesShared, listProfiles as listProfilesShared, setMachineProfile, } from "./profile-store.js";
-import { writeSkillMd, isManagedSymlink } from "./link-skills.js";
-import { syncScopeSkillsToDir } from "./skill-files.js";
-import { renderSkillInstructionsSection } from "./skill-registry.js";
-import { findProjectDir } from "./project-locator.js";
-import { getProjectOwnershipMode, readProjectConfig, } from "./project-config.js";
-import { writeContextDefault, writeContextDebugging, writeContextPlanning, writeContextClean, readBackNativeMemory, rebuildMemory, } from "./link-context.js";
+import { ROOT } from "../package-metadata.js";
+import { configureMcpTargets, ensureGovernanceFiles, getHooksEnabledPreference, getMcpEnabledPreference, isVersionNewer, patchJsonFile, setMcpEnabledPreference, } from "../init/init.js";
+import { configureAllHooks, detectInstalledTools } from "../hooks.js";
+import { getMachineName, persistMachineName } from "../machine-identity.js";
+import { debugLog, EXEC_TIMEOUT_MS, EXEC_TIMEOUT_QUICK_MS, isRecord, homePath, hookConfigPath, installPreferencesFile, atomicWriteText, } from "../shared.js";
+import { errorMessage } from "../utils.js";
+import { log } from "../init/shared.js";
+import { listMachines as listMachinesShared, listProfiles as listProfilesShared, setMachineProfile, } from "../profile-store.js";
+import { writeSkillMd, isManagedSymlink } from "./skills.js";
+import { syncScopeSkillsToDir } from "../skill/files.js";
+import { renderSkillInstructionsSection } from "../skill/registry.js";
+import { findProjectDir } from "../project-locator.js";
+import { getProjectOwnershipMode, readProjectConfig, } from "../project-config.js";
+import { writeContextDefault, writeContextDebugging, writeContextPlanning, writeContextClean, readBackNativeMemory, rebuildMemory, } from "./context.js";
+import { logger } from "../logger.js";
 // Re-export sub-modules so existing imports from "./link.js" continue to work
-export { runDoctor } from "./link-doctor.js";
-export { updateFileChecksums, verifyFileChecksums } from "./link-checksums.js";
-export { findProjectDir } from "./project-locator.js";
-export { parseSkillFrontmatter, validateSkillFrontmatter, validateSkillsDir, readSkillManifestHooks, } from "./link-skills.js";
+export { runDoctor } from "./doctor.js";
+export { updateFileChecksums, verifyFileChecksums } from "./checksums.js";
+export { findProjectDir } from "../project-locator.js";
+export { parseSkillFrontmatter, validateSkillFrontmatter, validateSkillsDir, readSkillManifestHooks, } from "./skills.js";
 // ── Helpers (exported for link-doctor) ──────────────────────────────────────
-export { getMachineName } from "./machine-identity.js";
+export { getMachineName } from "../machine-identity.js";
 export function lookupProfile(phrenPath, machine) {
     const listed = listMachinesShared(phrenPath);
     if (!listed.ok)
@@ -115,8 +116,7 @@ function setupSparseCheckout(phrenPath, projects) {
         execFileSync("git", ["rev-parse", "--git-dir"], { cwd: phrenPath, stdio: "ignore", timeout: EXEC_TIMEOUT_QUICK_MS });
     }
     catch (err) {
-        if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] setupSparseCheckout notAGitRepo: ${errorMessage(err)}\n`);
+        logger.debug("link", `setupSparseCheckout notAGitRepo: ${errorMessage(err)}`);
         return;
     }
     const alwaysInclude = ["profiles", "machines.yaml", "global", "scripts", "link.sh", "README.md", ".gitignore"];
@@ -268,8 +268,7 @@ function linkGlobal(phrenPath, tools) {
                 symlinkFile(globalClaude, path.join(copilotInstrDir, "copilot-instructions.md"), phrenPath);
             }
             catch (err) {
-                if ((process.env.PHREN_DEBUG))
-                    process.stderr.write(`[phren] linkGlobal copilotInstructions: ${errorMessage(err)}\n`);
+                logger.debug("link", `linkGlobal copilotInstructions: ${errorMessage(err)}`);
             }
         }
     }
@@ -314,8 +313,7 @@ function linkProject(phrenPath, project, tools) {
                         symlinkFile(src, path.join(copilotDir, "copilot-instructions.md"), phrenPath);
                     }
                     catch (err) {
-                        if ((process.env.PHREN_DEBUG))
-                            process.stderr.write(`[phren] linkProject copilotInstructions: ${errorMessage(err)}\n`);
+                        logger.debug("link", `linkProject copilotInstructions: ${errorMessage(err)}`);
                     }
                 }
             }
@@ -338,8 +336,7 @@ function linkProject(phrenPath, project, tools) {
             addTokenAnnotation(claudeFile);
         }
         catch (err) {
-            if ((process.env.PHREN_DEBUG))
-                process.stderr.write(`[phren] linkProject tokenAnnotation: ${errorMessage(err)}\n`);
+            logger.debug("link", `linkProject tokenAnnotation: ${errorMessage(err)}`);
         }
     }
     // Project-level skills
@@ -355,8 +352,7 @@ function linkProject(phrenPath, project, tools) {
                 excludeEntries.push("AGENTS.md");
         }
         catch (err) {
-            if ((process.env.PHREN_DEBUG))
-                process.stderr.write(`[phren] linkProject agentsMd: ${errorMessage(err)}\n`);
+            logger.debug("link", `linkProject agentsMd: ${errorMessage(err)}`);
         }
     }
     // Auto-exclude phren-managed files from git status
@@ -507,8 +503,7 @@ export async function runLink(phrenPath, opts = {}) {
         log(`  phren.SKILL.md written (agentskills-compatible tools)`);
     }
     catch (err) {
-        if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] link writeSkillMd: ${errorMessage(err)}\n`);
+        logger.debug("link", `link writeSkillMd: ${errorMessage(err)}`);
     }
     log("");
     // Step 7: Context file

package/mcp/dist/{link-skills.js → link/skills.js}

@@ -1,12 +1,13 @@
 import * as fs from "fs";
 import * as path from "path";
 import * as yaml from "js-yaml";
-import { debugLog } from "./shared.js";
-import { errorMessage } from "./utils.js";
-import { buildSharedLifecycleCommands } from "./hooks.js";
-import { VERSION } from "./package-metadata.js";
-import { getToolCount, renderToolCatalogMarkdown } from "./tool-registry.js";
-import { isSkillEnabled } from "./skill-state.js";
+import { debugLog } from "../shared.js";
+import { errorMessage } from "../utils.js";
+import { buildSharedLifecycleCommands } from "../hooks.js";
+import { VERSION } from "../package-metadata.js";
+import { getToolCount, renderToolCatalogMarkdown } from "../tool-registry.js";
+import { isSkillEnabled } from "../skill/state.js";
+import { logger } from "../logger.js";
 const REQUIRED_SKILL_FIELDS = ["name", "description"];
 export function parseSkillFrontmatter(rawContent) {
     // Normalize UTF-8 BOM and Windows-style CRLF line endings before matching frontmatter
@@ -190,8 +191,7 @@ function cleanupManagedSkillLinks(destDir, expectedNames, managedRoot) {
             fs.unlinkSync(destPath);
         }
         catch (err) {
-            if ((process.env.PHREN_DEBUG))
-                process.stderr.write(`[phren] cleanupManagedSkillLinks: ${errorMessage(err)}\n`);
+            logger.debug("link-skills", `cleanupManagedSkillLinks: ${errorMessage(err)}`);
         }
     }
 }
@@ -217,7 +217,7 @@ export function linkSkillsDir(srcDir, destDir, managedRoot, symlinkFile, opts) {
                     message: `Skipping skill '${skillName}' — user skill already exists at ${destPath}. To use phren's version, rename or remove your skill first.`,
                 };
                 collisions.push(collision);
-                process.stderr.write(`[phren] ${collision.message}\n`);
+                logger.warn("link-skills", collision.message);
                 continue;
             }
             expectedNames.add(entry);
@@ -234,7 +234,7 @@ export function linkSkillsDir(srcDir, destDir, managedRoot, symlinkFile, opts) {
                         message: `Skipping skill '${skillName}' — user skill already exists at ${destPath}. To use phren's version, rename or remove your skill first.`,
                     };
                     collisions.push(collision);
-                    process.stderr.write(`[phren] ${collision.message}\n`);
+                    logger.warn("link-skills", collision.message);
                     continue;
                 }
                 expectedNames.add(entry);

package/mcp/dist/logger.js

@@ -1,11 +1,13 @@
 import * as fs from "fs";
 import { runtimeFile, findPhrenPath } from "./shared.js";
+let _cachedPhrenPath;
 export function log(level, tool, message, extra) {
     try {
-        const phrenPath = findPhrenPath();
-        if (!phrenPath)
+        if (_cachedPhrenPath === undefined)
+            _cachedPhrenPath = findPhrenPath();
+        if (!_cachedPhrenPath)
             return;
-        const logPath = runtimeFile(phrenPath, "debug.log");
+        const logPath = runtimeFile(_cachedPhrenPath, "debug.log");
         const line = JSON.stringify({ ts: new Date().toISOString(), level, tool, message, ...extra });
         fs.appendFileSync(logPath, line + "\n");
     }
@@ -13,3 +15,9 @@ export function log(level, tool, message, extra) {
         // Logging must never throw
     }
 }
+export const logger = {
+    debug: (tool, message, extra) => log("debug", tool, message, extra),
+    info: (tool, message, extra) => log("info", tool, message, extra),
+    warn: (tool, message, extra) => log("warn", tool, message, extra),
+    error: (tool, message, extra) => log("error", tool, message, extra),
+};

package/mcp/dist/phren-art.js

@@ -13,11 +13,7 @@ const RESET = `${ESC}0m`;
 const PURPLE = `${ESC}35m`; // magenta — body
 const BRIGHT_PURPLE = `${ESC}95m`; // bright magenta — highlights
 const CYAN = `${ESC}96m`; // bright cyan — sparkle
-const DIM = `${ESC}2m`;
 const DARK_PURPLE = `${ESC}38;5;57m`; // deep purple — shadow/outline
-const LIGHT_PURPLE = `${ESC}38;5;141m`; // lavender — brain highlights
-const MID_PURPLE = `${ESC}38;5;98m`; // mid tone
-const NAVY = `${ESC}38;5;18m`; // darkest outline
 // ── Art constants (24px wide, truecolor half-blocks) ─────────────────────────
 /**
  * Phren truecolor art (24px wide, generated from phren-transparent.png).
@@ -38,8 +34,6 @@ export const PHREN_ART = [
     "                        ",
     "                        ",
 ];
-/** The art width in visible columns */
-const ART_WIDTH = 24;
 // ── Sparkle row: the cyan pixels at row 2 ────────────────────────────────────
 // Sparkle uses ▄ half-blocks with cyan truecolor. For animation we cycle through
 // decorative unicode characters at different brightness levels.

package/mcp/dist/phren-paths.js

@@ -7,6 +7,10 @@ import { bootstrapPhrenDotEnv } from "./phren-dotenv.js";
 import { PhrenError, isRecord, RESERVED_PROJECT_DIR_NAMES } from "./phren-core.js";
 import { errorMessage, isValidProjectName, safeProjectPath } from "./utils.js";
 bootstrapPhrenDotEnv();
+function stderrLog(msg) { try {
+    process.stderr.write("[phren] " + msg + "\n");
+}
+catch { } }
 export const ROOT_MANIFEST_FILENAME = "phren.root.yaml";
 export function homeDir() {
     return process.env.HOME || process.env.USERPROFILE || os.homedir();
@@ -75,7 +79,7 @@ export function readRootManifest(phrenPath) {
     }
     catch (err) {
         if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] readRootManifest: ${errorMessage(err)}\n`);
+            stderrLog(`readRootManifest: ${errorMessage(err)}`);
         return null;
     }
 }
@@ -263,6 +267,20 @@ export function debugLog(msg) {
         // debug log is best-effort; logging errors about logging would recurse
     }
 }
+/** Always-on structured error log (no PHREN_DEBUG gate). */
+export function errorLog(tool, msg) {
+    try {
+        const phrenPath = findPhrenPath();
+        if (!phrenPath)
+            return;
+        const logFile = runtimeFile(phrenPath, "debug.log");
+        const line = JSON.stringify({ ts: new Date().toISOString(), level: "error", tool, message: msg });
+        fs.appendFileSync(logFile, line + "\n");
+    }
+    catch {
+        // Logging must never throw
+    }
+}
 export function appendIndexEvent(phrenPath, event) {
     try {
         const file = runtimeFile(phrenPath, "index-events.jsonl");
@@ -270,7 +288,7 @@ export function appendIndexEvent(phrenPath, event) {
     }
     catch (err) {
         if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] appendIndexEvent: ${errorMessage(err)}\n`);
+            stderrLog(`appendIndexEvent: ${errorMessage(err)}`);
     }
 }
 /** Resolve the canonical findings file for a project directory. */
@@ -301,7 +319,7 @@ export function findProjectNameCaseInsensitive(phrenPath, name) {
     }
     catch (err) {
         if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] findProjectNameCaseInsensitive: ${errorMessage(err)}\n`);
+            stderrLog(`findProjectNameCaseInsensitive: ${errorMessage(err)}`);
     }
     return null;
 }
@@ -318,7 +336,7 @@ export function findArchivedProjectNameCaseInsensitive(phrenPath, name) {
     }
     catch (err) {
         if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] findArchivedProjectNameCaseInsensitive: ${errorMessage(err)}\n`);
+            stderrLog(`findArchivedProjectNameCaseInsensitive: ${errorMessage(err)}`);
     }
     return null;
 }
@@ -342,26 +360,26 @@ export function getProjectDirs(phrenPath, profile) {
     }
     if (profile) {
         if (!isValidProjectName(profile)) {
-            console.error(`${PhrenError.VALIDATION_ERROR}: Invalid PHREN_PROFILE value: ${profile}`);
+            errorLog("getProjectDirs", `${PhrenError.VALIDATION_ERROR}: Invalid PHREN_PROFILE value: ${profile}`);
             return [];
         }
         const profilePath = path.join(phrenPath, "profiles", `${profile}.yaml`);
         if (!fs.existsSync(profilePath)) {
-            console.error(`${PhrenError.FILE_NOT_FOUND}: Profile file not found: ${profilePath}`);
+            errorLog("getProjectDirs", `${PhrenError.FILE_NOT_FOUND}: Profile file not found: ${profilePath}`);
             return [];
         }
         try {
             const data = yaml.load(fs.readFileSync(profilePath, "utf-8"), { schema: yaml.CORE_SCHEMA });
             const projects = isRecord(data) ? data.projects : undefined;
             if (!Array.isArray(projects)) {
-                console.error(`${PhrenError.MALFORMED_YAML}: Profile YAML missing valid "projects" array: ${profilePath}`);
+                errorLog("getProjectDirs", `${PhrenError.MALFORMED_YAML}: Profile YAML missing valid "projects" array: ${profilePath}`);
                 return [];
             }
             const listed = projects
                 .map((p) => {
                 const name = String(p);
                 if (!isValidProjectName(name)) {
-                    console.error(`${PhrenError.VALIDATION_ERROR}: Skipping invalid project name in profile: ${name}`);
+                    errorLog("getProjectDirs", `${PhrenError.VALIDATION_ERROR}: Skipping invalid project name in profile: ${name}`);
                     return null;
                 }
                 return safeProjectPath(phrenPath, name);
@@ -374,8 +392,8 @@ export function getProjectDirs(phrenPath, profile) {
         }
         catch (err) {
             if ((process.env.PHREN_DEBUG))
-                process.stderr.write(`[phren] getProjectDirs yamlParse: ${errorMessage(err)}\n`);
-            console.error(`${PhrenError.MALFORMED_YAML}: Malformed profile YAML: ${profilePath}`);
+                stderrLog(`getProjectDirs yamlParse: ${errorMessage(err)}`);
+            errorLog("getProjectDirs", `${PhrenError.MALFORMED_YAML}: Malformed profile YAML: ${profilePath}`);
             return [];
         }
     }
@@ -386,7 +404,7 @@ export function getProjectDirs(phrenPath, profile) {
     }
     catch (err) {
         if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] getProjectDirs: ${errorMessage(err)}\n`);
+            stderrLog(`getProjectDirs: ${errorMessage(err)}`);
         return [];
     }
 }
@@ -413,7 +431,7 @@ export function collectNativeMemoryFiles() {
     }
     catch (err) {
         if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] collectNativeMemoryFiles: ${errorMessage(err)}\n`);
+            stderrLog(`collectNativeMemoryFiles: ${errorMessage(err)}`);
     }
     return results;
 }

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;

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

@@ -2,7 +2,7 @@ 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";
 const TOPIC_CONFIG_FILENAME = "topic-config.json";
 const AUTO_TOPIC_MARKER_RE = /^<!--\s*phren:auto-topic(?:\s+slug=([a-z0-9_-]+))?\s*-->$/;

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/{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);

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}

@@ -1,8 +1,9 @@
-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";
 export function escapeRegex(s) { return s.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); }
 /** Escape SQL LIKE wildcard characters so user input is treated literally. */
 export function escapeLike(s) { return s.replace(/[%_\\]/g, '\\$&'); }
@@ -116,8 +117,7 @@ function getOrCreateFragment(db, name, type) {
         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 +139,7 @@ export function ensureGlobalEntitiesTable(db) {
       )`);
     }
     catch (err) {
-        if (process.env.PHREN_DEBUG)
-            process.stderr.write(`[phren] ensureGlobalEntitiesTable: ${errorMessage(err)}\n`);
+        logger.debug("ensureGlobalEntitiesTable", errorMessage(err));
     }
 }
 /**
@@ -186,8 +185,7 @@ 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, []);
         }
     }
@@ -225,8 +223,7 @@ 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);
@@ -236,8 +233,7 @@ 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 [];
     }
 }
@@ -353,8 +349,7 @@ 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) {
@@ -362,8 +357,7 @@ 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));
             }
         }
     }
@@ -391,8 +385,7 @@ 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 };
 }
@@ -427,8 +420,7 @@ 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;
 }
@@ -448,8 +440,7 @@ 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();
     }
 }

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';