@phren/cli 0.0.27 → 0.0.32

package/mcp/dist/{cli-hooks-session.js → cli/hooks-session.js}

@@ -1,20 +1,21 @@
-import { buildHookContext, handleGuardSkip, debugLog, appendAuditLog, runtimeFile, sessionMarker, EXEC_TIMEOUT_MS, getPhrenPath, getProjectDirs, findProjectNameCaseInsensitive, homePath, updateRuntimeHealth, withFileLock, getWorkflowPolicy, appendReviewQueue, recordFeedback, getQualityMultiplier, detectProject, isProjectHookEnabled, readProjectConfig, getProjectSourcePath, detectProjectDir, ensureLocalGitRepo, isProjectTracked, repairPreexistingInstall, getProactivityLevelForTask, getProactivityLevelForFindings, hasExplicitFindingSignal, shouldAutoCaptureFindingsForLevel, FINDING_SENSITIVITY_CONFIG, isFeatureEnabled, errorMessage, bootstrapPhrenDotEnv, finalizeTaskSession, appendFindingJournal, runDoctor, resolveRuntimeProfile, } from "./cli-hooks-context.js";
-import { sessionMetricsFile, qualityMarkers, } from "./shared.js";
-import { autoMergeConflicts, mergeTask, mergeFindings, } from "./shared-content.js";
-import { runGit } from "./utils.js";
-import { readInstallPreferences } from "./init-preferences.js";
+import { buildHookContext, handleGuardSkip, debugLog, appendAuditLog, runtimeFile, sessionMarker, EXEC_TIMEOUT_MS, getPhrenPath, getProjectDirs, findProjectNameCaseInsensitive, homePath, updateRuntimeHealth, withFileLock, getWorkflowPolicy, appendReviewQueue, recordFeedback, getQualityMultiplier, detectProject, isProjectHookEnabled, readProjectConfig, getProjectSourcePath, detectProjectDir, ensureLocalGitRepo, isProjectTracked, repairPreexistingInstall, getProactivityLevelForTask, getProactivityLevelForFindings, hasExplicitFindingSignal, shouldAutoCaptureFindingsForLevel, FINDING_SENSITIVITY_CONFIG, isFeatureEnabled, errorMessage, bootstrapPhrenDotEnv, finalizeTaskSession, appendFindingJournal, runDoctor, resolveRuntimeProfile, } from "./hooks-context.js";
+import { sessionMetricsFile, qualityMarkers, } from "../shared.js";
+import { autoMergeConflicts, mergeTask, mergeFindings, } from "../shared/content.js";
+import { runGit } from "../utils.js";
+import { readInstallPreferences } from "../init/preferences.js";
 import * as fs from "fs";
 import * as path from "path";
 import * as os from "os";
 import { execFileSync, spawn } from "child_process";
 import { fileURLToPath } from "url";
-import { isTaskFileName, TASKS_FILENAME } from "./data-tasks.js";
-import { buildIndex, queryRows, } from "./shared-index.js";
-import { filterTaskByPriority } from "./shared-retrieval.js";
+import { isTaskFileName, TASKS_FILENAME } from "../data/tasks.js";
+import { buildIndex, queryRows, } from "../shared/index.js";
+import { filterTaskByPriority } from "../shared/retrieval.js";
+import { logger } from "../logger.js";
 function getRuntimeProfile() {
     return resolveRuntimeProfile(getPhrenPath());
 }
-export { buildHookContext, checkHookGuard, handleGuardSkip } from "./cli-hooks-context.js";
+export { buildHookContext, checkHookGuard, handleGuardSkip } from "./hooks-context.js";
 /** Read JSON from stdin if it's not a TTY. Returns null if stdin is a TTY or parsing fails. */
 function readStdinJson() {
     if (process.stdin.isTTY)
@@ -23,8 +24,7 @@ function readStdinJson() {
         return JSON.parse(fs.readFileSync(0, "utf-8"));
     }
     catch (err) {
-        if (process.env.PHREN_DEBUG)
-            process.stderr.write(`[phren] readStdinJson: ${errorMessage(err)}\n`);
+        logger.debug("hooks-session", `readStdinJson: ${errorMessage(err)}`);
         return null;
     }
 }
@@ -230,13 +230,17 @@ export function trackSessionMetrics(phrenPathLocal, sessionId, selected) {
 }
 // ── Background maintenance ───────────────────────────────────────────────────
 export function resolveSubprocessArgs(command) {
-    const distEntry = path.join(path.dirname(fileURLToPath(import.meta.url)), "index.js");
-    if (fs.existsSync(distEntry))
-        return [distEntry, command];
-    const sourceEntry = process.argv.find((a) => /[\\/]index\.(ts|js)$/.test(a) && fs.existsSync(a));
-    const runner = process.argv[1];
-    if (sourceEntry && runner)
-        return [runner, sourceEntry, command];
+    // Prefer the entry script that started this process
+    const entry = process.argv[1];
+    if (entry && fs.existsSync(entry) && /index\.(ts|js)$/.test(entry))
+        return [entry, command];
+    // Fallback: look for index.js next to this file or one level up (for subdirectory builds)
+    const thisDir = path.dirname(fileURLToPath(import.meta.url));
+    for (const dir of [thisDir, path.dirname(thisDir)]) {
+        const candidate = path.join(dir, "index.js");
+        if (fs.existsSync(candidate))
+            return [candidate, command];
+    }
     return null;
 }
 function scheduleBackgroundSync(phrenPathLocal) {
@@ -319,8 +323,7 @@ function scheduleBackgroundMaintenance(phrenPathLocal, project) {
         }
         catch (err) {
             // Another process already claimed the lock
-            if (process.env.PHREN_DEBUG)
-                process.stderr.write(`[phren] backgroundMaintenance lockClaim: ${errorMessage(err)}\n`);
+            logger.debug("hooks-session", `backgroundMaintenance lockClaim: ${errorMessage(err)}`);
             return false;
         }
         try {
@@ -352,24 +355,21 @@ function scheduleBackgroundMaintenance(phrenPathLocal, project) {
                 fs.appendFileSync(logPath, msg);
             }
             catch (err) {
-                if (process.env.PHREN_DEBUG)
-                    process.stderr.write(`[phren] backgroundMaintenance exitLog: ${errorMessage(err)}\n`);
+                logger.debug("hooks-session", `backgroundMaintenance exitLog: ${errorMessage(err)}`);
             }
             if (code === 0) {
                 try {
                     fs.writeFileSync(markers.done, new Date().toISOString() + "\n");
                 }
                 catch (err) {
-                    if (process.env.PHREN_DEBUG)
-                        process.stderr.write(`[phren] backgroundMaintenance doneMarker: ${errorMessage(err)}\n`);
+                    logger.debug("hooks-session", `backgroundMaintenance doneMarker: ${errorMessage(err)}`);
                 }
             }
             try {
                 fs.unlinkSync(markers.lock);
             }
             catch (err) {
-                if (process.env.PHREN_DEBUG)
-                    process.stderr.write(`[phren] backgroundMaintenance unlockOnExit: ${errorMessage(err)}\n`);
+                logger.debug("hooks-session", `backgroundMaintenance unlockOnExit: ${errorMessage(err)}`);
             }
         });
         child.on("error", (spawnErr) => {
@@ -378,15 +378,13 @@ function scheduleBackgroundMaintenance(phrenPathLocal, project) {
                 fs.appendFileSync(logPath, msg);
             }
             catch (err) {
-                if (process.env.PHREN_DEBUG)
-                    process.stderr.write(`[phren] backgroundMaintenance errorLog: ${errorMessage(err)}\n`);
+                logger.debug("hooks-session", `backgroundMaintenance errorLog: ${errorMessage(err)}`);
             }
             try {
                 fs.unlinkSync(markers.lock);
             }
             catch (err) {
-                if (process.env.PHREN_DEBUG)
-                    process.stderr.write(`[phren] backgroundMaintenance unlockOnError: ${errorMessage(err)}\n`);
+                logger.debug("hooks-session", `backgroundMaintenance unlockOnError: ${errorMessage(err)}`);
             }
         });
         fs.closeSync(logFd);
@@ -401,15 +399,13 @@ function scheduleBackgroundMaintenance(phrenPathLocal, project) {
             fs.appendFileSync(path.join(logDir, "background-maintenance.log"), `[${new Date().toISOString()}] spawn failed: ${errMsg}\n`);
         }
         catch (err) {
-            if (process.env.PHREN_DEBUG)
-                process.stderr.write(`[phren] backgroundMaintenance logSpawnFailure: ${errorMessage(err)}\n`);
+            logger.debug("hooks-session", `backgroundMaintenance logSpawnFailure: ${errorMessage(err)}`);
         }
         try {
             fs.unlinkSync(markers.lock);
         }
         catch (err) {
-            if (process.env.PHREN_DEBUG)
-                process.stderr.write(`[phren] backgroundMaintenance unlockOnFailure: ${errorMessage(err)}\n`);
+            logger.debug("hooks-session", `backgroundMaintenance unlockOnFailure: ${errorMessage(err)}`);
         }
         return false;
     }
@@ -608,12 +604,11 @@ export async function handleHookSessionStart() {
     const maintenanceScheduled = scheduleBackgroundMaintenance(phrenPath);
     const unsyncedCommits = hasRemote ? await countUnsyncedCommits(phrenPath) : 0;
     try {
-        const { trackSession } = await import("./telemetry.js");
+        const { trackSession } = await import("../telemetry.js");
         trackSession(phrenPath);
     }
     catch (err) {
-        if (process.env.PHREN_DEBUG)
-            process.stderr.write(`[phren] hookSessionStart trackSession: ${errorMessage(err)}\n`);
+        logger.debug("hooks-session", `hookSessionStart trackSession: ${errorMessage(err)}`);
     }
     updateRuntimeHealth(phrenPath, {
         lastSessionStartAt: startedAt,
@@ -779,8 +774,7 @@ export async function handleHookStop() {
                             }
                         }
                         catch (err) {
-                            if (process.env.PHREN_DEBUG)
-                                process.stderr.write(`[phren] hookStop transcriptParse: ${errorMessage(err)}\n`);
+                            logger.debug("hooks-session", `hookStop transcriptParse: ${errorMessage(err)}`);
                         }
                     }
                     captureInput = assistantTexts.join("\n");
@@ -804,8 +798,7 @@ export async function handleHookStop() {
                             }
                         }
                         catch (err) {
-                            if (process.env.PHREN_DEBUG)
-                                process.stderr.write(`[phren] hookStop sessionCapCheck: ${errorMessage(err)}\n`);
+                            logger.debug("hooks-session", `hookStop sessionCapCheck: ${errorMessage(err)}`);
                         }
                     }
                     if (!capReached) {
@@ -1225,8 +1218,7 @@ export async function handleHookTool() {
                 raw = fs.readFileSync(0, "utf-8");
             }
             catch (err) {
-                if (process.env.PHREN_DEBUG)
-                    process.stderr.write(`[phren] hookTool stdinRead: ${errorMessage(err)}\n`);
+                logger.debug("hooks-session", `hookTool stdinRead: ${errorMessage(err)}`);
                 process.exit(0);
             }
         }
@@ -1235,8 +1227,7 @@ export async function handleHookTool() {
             data = JSON.parse(raw);
         }
         catch (err) {
-            if (process.env.PHREN_DEBUG)
-                process.stderr.write(`[phren] hookTool stdinParse: ${errorMessage(err)}\n`);
+            logger.debug("hooks-session", `hookTool stdinParse: ${errorMessage(err)}`);
             process.exit(0);
         }
         const toolName = String(data.tool_name ?? data.tool ?? "");
@@ -1287,8 +1278,7 @@ export async function handleHookTool() {
             fs.appendFileSync(logFile, JSON.stringify(entry) + "\n");
         }
         catch (err) {
-            if (process.env.PHREN_DEBUG)
-                process.stderr.write(`[phren] hookTool toolLog: ${errorMessage(err)}\n`);
+            logger.debug("hooks-session", `hookTool toolLog: ${errorMessage(err)}`);
         }
         const cooldownFile = runtimeFile(ctx.phrenPath, "hook-tool-cooldown");
         try {
@@ -1301,8 +1291,7 @@ export async function handleHookTool() {
             }
         }
         catch (err) {
-            if (process.env.PHREN_DEBUG)
-                process.stderr.write(`[phren] hookTool cooldownStat: ${errorMessage(err)}\n`);
+            logger.debug("hooks-session", `hookTool cooldownStat: ${errorMessage(err)}`);
         }
         if (activeProject && sessionId) {
             try {
@@ -1318,8 +1307,7 @@ export async function handleHookTool() {
                 }
             }
             catch (err) {
-                if (process.env.PHREN_DEBUG)
-                    process.stderr.write(`[phren] hookTool sessionCapCheck: ${errorMessage(err)}\n`);
+                logger.debug("hooks-session", `hookTool sessionCapCheck: ${errorMessage(err)}`);
             }
         }
         const findingsLevelForTool = getProactivityLevelForFindings(ctx.phrenPath);
@@ -1335,8 +1323,7 @@ export async function handleHookTool() {
                         fs.writeFileSync(cooldownFile, Date.now().toString());
                     }
                     catch (err) {
-                        if (process.env.PHREN_DEBUG)
-                            process.stderr.write(`[phren] hookTool cooldownWrite: ${errorMessage(err)}\n`);
+                        logger.debug("hooks-session", `hookTool cooldownWrite: ${errorMessage(err)}`);
                     }
                     if (sessionId) {
                         try {
@@ -1346,15 +1333,13 @@ export async function handleHookTool() {
                                 count = Number.parseInt(fs.readFileSync(capFile, "utf8").trim(), 10) || 0;
                             }
                             catch (err) {
-                                if (process.env.PHREN_DEBUG)
-                                    process.stderr.write(`[phren] hookTool capFileRead: ${errorMessage(err)}\n`);
+                                logger.debug("hooks-session", `hookTool capFileRead: ${errorMessage(err)}`);
                             }
                             count += candidates.length;
                             fs.writeFileSync(capFile, count.toString());
                         }
                         catch (err) {
-                            if (process.env.PHREN_DEBUG)
-                                process.stderr.write(`[phren] hookTool capFileWrite: ${errorMessage(err)}\n`);
+                            logger.debug("hooks-session", `hookTool capFileWrite: ${errorMessage(err)}`);
                         }
                     }
                 }

package/mcp/dist/{cli-hooks.js → cli/hooks.js}

@@ -4,38 +4,39 @@
 //   cli-hooks-session.ts    — session lifecycle hooks, metrics, background maintenance
 //   cli-hooks-output.ts     — hook output formatting
 //   cli-hooks-globs.ts      — project glob matching
-import { debugLog, sessionMarker, sessionsDir, getPhrenPath, } from "./shared.js";
-import { mergeConfig, } from "./shared-governance.js";
-import { buildIndex, detectProject, } from "./shared-index.js";
-import { isProjectHookEnabled } from "./project-config.js";
-import { checkConsolidationNeeded, } from "./shared-content.js";
-import { buildRobustFtsQuery, extractKeywordEntries, isFeatureEnabled, clampInt, errorMessage, loadSynonymMap, learnSynonym, STOP_WORDS, } from "./utils.js";
-import { getHooksEnabledPreference } from "./init.js";
-import { isToolHookEnabled } from "./hooks.js";
-import { handleExtractMemories } from "./cli-extract.js";
-import { appendAuditLog } from "./shared.js";
-import { updateRuntimeHealth } from "./shared-governance.js";
-import { getProactivityLevelForTask, getProactivityLevelForFindings } from "./proactivity.js";
-import { FINDING_SENSITIVITY_CONFIG } from "./cli-config.js";
+import { debugLog, sessionMarker, sessionsDir, getPhrenPath, } from "../shared.js";
+import { mergeConfig, } from "../shared/governance.js";
+import { buildIndex, detectProject, } from "../shared/index.js";
+import { isProjectHookEnabled } from "../project-config.js";
+import { checkConsolidationNeeded, } from "../shared/content.js";
+import { buildRobustFtsQuery, extractKeywordEntries, isFeatureEnabled, clampInt, errorMessage, loadSynonymMap, learnSynonym, STOP_WORDS, } from "../utils.js";
+import { getHooksEnabledPreference } from "../init/init.js";
+import { logger } from "../logger.js";
+import { isToolHookEnabled } from "../hooks.js";
+import { handleExtractMemories } from "./extract.js";
+import { appendAuditLog } from "../shared.js";
+import { updateRuntimeHealth } from "../shared/governance.js";
+import { getProactivityLevelForTask, getProactivityLevelForFindings } from "../proactivity.js";
+import { FINDING_SENSITIVITY_CONFIG } from "./config.js";
 import * as fs from "fs";
 // ── Re-exports from focused modules ─────────────────────────────────────────
 // Citations
-export { parseCitations, validateCitation, annotateStale, clearCitationValidCache, } from "./cli-hooks-citations.js";
+export { parseCitations, validateCitation, annotateStale, clearCitationValidCache, } from "./hooks-citations.js";
 // Globs
-export { getProjectGlobBoost, clearProjectGlobCache, } from "./cli-hooks-globs.js";
+export { getProjectGlobBoost, clearProjectGlobCache, } from "./hooks-globs.js";
 // Retrieval
-export { detectTaskIntent, filterTaskByPriority, searchDocuments, applyTrustFilter, rankResults, selectSnippets, } from "./shared-retrieval.js";
+export { detectTaskIntent, filterTaskByPriority, searchDocuments, applyTrustFilter, rankResults, selectSnippets, } from "../shared/retrieval.js";
 // Output
-export { buildHookOutput, } from "./cli-hooks-output.js";
+export { buildHookOutput, } from "./hooks-output.js";
 // Session
-export { handleHookSessionStart, handleHookStop, handleBackgroundSync, handleHookContext, handleHookTool, trackSessionMetrics, filterConversationInsightsForProactivity, extractToolFindings, filterToolFindingsForProactivity, resolveSubprocessArgs, } from "./cli-hooks-session.js";
+export { handleHookSessionStart, handleHookStop, handleBackgroundSync, handleHookContext, handleHookTool, trackSessionMetrics, filterConversationInsightsForProactivity, extractToolFindings, filterToolFindingsForProactivity, resolveSubprocessArgs, } from "./hooks-session.js";
 // ── Imports for the orchestrator ─────────────────────────────────────────────
-import { searchDocumentsAsync, applyTrustFilter, rankResults, selectSnippets, detectTaskIntent, } from "./shared-retrieval.js";
-import { buildHookOutput } from "./cli-hooks-output.js";
-import { getGitContext, trackSessionMetrics, } from "./cli-hooks-session.js";
-import { approximateTokens } from "./shared-retrieval.js";
-import { resolveRuntimeProfile } from "./runtime-profile.js";
-import { handleTaskPromptLifecycle } from "./task-lifecycle.js";
+import { searchDocumentsAsync, applyTrustFilter, rankResults, selectSnippets, detectTaskIntent, } from "../shared/retrieval.js";
+import { buildHookOutput } from "./hooks-output.js";
+import { getGitContext, trackSessionMetrics, } from "./hooks-session.js";
+import { approximateTokens } from "../shared/retrieval.js";
+import { resolveRuntimeProfile } from "../runtime-profile.js";
+import { handleTaskPromptLifecycle } from "../task/lifecycle.js";
 function synonymTermKnown(term, map) {
     if (Object.prototype.hasOwnProperty.call(map, term))
         return true;
@@ -126,7 +127,7 @@ export async function handleHookPrompt() {
     }
     catch (err) {
         if (process.env.PHREN_DEBUG)
-            process.stderr.write(`[phren] hookPrompt stdinRead: ${errorMessage(err)}\n`);
+            logger.debug("cli-hooks", `hookPrompt stdinRead: ${errorMessage(err)}`);
         process.exit(0);
     }
     const input = parseHookInput(raw);
@@ -362,7 +363,7 @@ export async function handleHookPrompt() {
                 }
                 catch (err) {
                     if (process.env.PHREN_DEBUG)
-                        process.stderr.write(`[phren] hookPrompt noticeFileWrite: ${errorMessage(err)}\n`);
+                        logger.debug("cli-hooks", `hookPrompt noticeFileWrite: ${errorMessage(err)}`);
                 }
             }
         }

package/mcp/dist/{cli-namespaces.js → cli/namespaces.js}

@@ -1,20 +1,21 @@
 import * as fs from "fs";
 import * as path from "path";
 import { execFileSync } from "child_process";
-import { expandHomePath, findArchivedProjectNameCaseInsensitive, findProjectNameCaseInsensitive, getPhrenPath, getProjectDirs, homePath, hookConfigPath, normalizeProjectNameForCreate, readRootManifest, } from "./shared.js";
-import { isValidProjectName, errorMessage } from "./utils.js";
-import { readInstallPreferences, writeInstallPreferences } from "./init-preferences.js";
-import { buildSkillManifest, findLocalSkill, findSkill, getAllSkills } from "./skill-registry.js";
-import { detectSkillCollisions } from "./link-skills.js";
-import { setSkillEnabledAndSync, syncSkillLinksForScope } from "./skill-files.js";
-import { findProjectDir } from "./project-locator.js";
-import { TASK_FILE_ALIASES, addTask, completeTask, updateTask, reorderTask, pinTask, removeTask, workNextTask, tidyDoneTasks, linkTaskIssue, promoteTask, resolveTaskItem } from "./data-tasks.js";
-import { buildTaskIssueBody, createGithubIssueForTask, parseGithubIssueUrl, resolveProjectGithubRepo } from "./tasks-github.js";
-import { PROJECT_HOOK_EVENTS, PROJECT_OWNERSHIP_MODES, isProjectHookEnabled, parseProjectOwnershipMode, readProjectConfig, writeProjectConfig, writeProjectHookConfig, } from "./project-config.js";
-import { addFinding, removeFinding } from "./core-finding.js";
-import { supersedeFinding, retractFinding, resolveFindingContradiction } from "./finding-lifecycle.js";
-import { readCustomHooks, getHookTarget, HOOK_EVENT_VALUES, validateCustomHookCommand } from "./hooks.js";
-import { runtimeFile } from "./shared.js";
+import { expandHomePath, findArchivedProjectNameCaseInsensitive, findProjectNameCaseInsensitive, getPhrenPath, getProjectDirs, homePath, hookConfigPath, normalizeProjectNameForCreate, readRootManifest, } from "../shared.js";
+import { isValidProjectName, errorMessage } from "../utils.js";
+import { logger } from "../logger.js";
+import { readInstallPreferences, writeInstallPreferences } from "../init/preferences.js";
+import { buildSkillManifest, findLocalSkill, findSkill, getAllSkills } from "../skill/registry.js";
+import { detectSkillCollisions } from "../link/skills.js";
+import { setSkillEnabledAndSync, syncSkillLinksForScope } from "../skill/files.js";
+import { findProjectDir } from "../project-locator.js";
+import { TASK_FILE_ALIASES, addTask, completeTask, updateTask, reorderTask, pinTask, removeTask, workNextTask, tidyDoneTasks, linkTaskIssue, promoteTask, resolveTaskItem } from "../data/tasks.js";
+import { buildTaskIssueBody, createGithubIssueForTask, parseGithubIssueUrl, resolveProjectGithubRepo } from "../task/github.js";
+import { PROJECT_HOOK_EVENTS, PROJECT_OWNERSHIP_MODES, isProjectHookEnabled, parseProjectOwnershipMode, readProjectConfig, writeProjectConfig, writeProjectHookConfig, } from "../project-config.js";
+import { addFinding, removeFinding } from "../core/finding.js";
+import { supersedeFinding, retractFinding, resolveFindingContradiction } from "../finding/lifecycle.js";
+import { readCustomHooks, getHookTarget, HOOK_EVENT_VALUES, validateCustomHookCommand } from "../hooks.js";
+import { runtimeFile } from "../shared.js";
 const HOOK_TOOLS = ["claude", "copilot", "cursor", "codex"];
 function printSkillsUsage() {
     console.log("Usage:");
@@ -78,7 +79,7 @@ function openInEditor(filePath) {
     }
     catch (err) {
         if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] openInEditor: ${errorMessage(err)}\n`);
+            logger.debug("cli-namespaces", `openInEditor: ${errorMessage(err)}`);
         console.error(`Editor "${editor}" failed. Set $EDITOR to your preferred editor.`);
         process.exit(1);
     }
@@ -147,7 +148,7 @@ export function handleSkillsNamespace(args, profile) {
         }
         catch (err) {
             if ((process.env.PHREN_DEBUG))
-                process.stderr.write(`[phren] skill add symlinkFailed: ${errorMessage(err)}\n`);
+                logger.debug("cli-namespaces", `skill add symlinkFailed: ${errorMessage(err)}`);
             fs.copyFileSync(source, dest);
             console.log(`Copied skill ${fileName} into ${project}.`);
         }
@@ -457,7 +458,7 @@ export function handleDetectSkills(args, profile) {
         }
         catch (err) {
             if ((process.env.PHREN_DEBUG))
-                process.stderr.write(`[phren] skillList lstat: ${errorMessage(err)}\n`);
+                logger.debug("cli-namespaces", `skillList lstat: ${errorMessage(err)}`);
         }
         const name = entry.replace(/\.md$/, "");
         if (trackedSkills.has(name))
@@ -666,7 +667,7 @@ export async function handleProjectsNamespace(args, profile) {
             console.error(`Project "${name}" not found.`);
             process.exit(1);
         }
-        const { readFindings, readTasks, resolveTaskFilePath, TASKS_FILENAME } = await import("./data-access.js");
+        const { readFindings, readTasks, resolveTaskFilePath, TASKS_FILENAME } = await import("../data/access.js");
         const exported = { project: name, exportedAt: new Date().toISOString(), version: 1 };
         const summaryPath = path.join(projectDir, "summary.md");
         if (fs.existsSync(summaryPath))
@@ -721,7 +722,7 @@ export async function handleProjectsNamespace(args, profile) {
             console.error("Invalid import payload: missing project field.");
             process.exit(1);
         }
-        const { TASKS_FILENAME } = await import("./data-access.js");
+        const { TASKS_FILENAME } = await import("../data/access.js");
         const phrenPath = getPhrenPath();
         const projectName = normalizeProjectNameForCreate(String(decoded.project));
         if (!isValidProjectName(projectName)) {
@@ -874,7 +875,7 @@ function handleProjectsList(profile) {
         }
         catch (err) {
             if ((process.env.PHREN_DEBUG))
-                process.stderr.write(`[phren] projects list readdir: ${errorMessage(err)}\n`);
+                logger.debug("cli-namespaces", `projects list readdir: ${errorMessage(err)}`);
             dirFiles = new Set();
         }
         const tags = [];
@@ -917,7 +918,7 @@ async function handleProjectsRemove(name, profile) {
     }
     catch (err) {
         if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] projects remove countFiles: ${errorMessage(err)}\n`);
+            logger.debug("cli-namespaces", `projects remove countFiles: ${errorMessage(err)}`);
     }
     const readline = await import("readline");
     const rl = readline.createInterface({ input: process.stdin, output: process.stdout });
@@ -956,7 +957,7 @@ export async function handleTaskNamespace(args) {
     }
     if (subcommand === "list") {
         // Delegate to the cross-project task view (same as `phren tasks`)
-        const { handleTaskView } = await import("./cli-ops.js");
+        const { handleTaskView } = await import("./ops.js");
         return handleTaskView(args[1] || "default");
     }
     if (subcommand === "add") {
@@ -1321,7 +1322,7 @@ export async function handleFindingNamespace(args) {
             console.error("Usage: phren finding list <project>");
             process.exit(1);
         }
-        const { readFindings } = await import("./data-access.js");
+        const { readFindings } = await import("../data/access.js");
         const result = readFindings(getPhrenPath(), project);
         if (!result.ok) {
             console.error(result.error);
@@ -1441,7 +1442,7 @@ export async function handleFindingNamespace(args) {
         const project = args[1];
         const phrenPath = getPhrenPath();
         const RESERVED_DIRS = new Set(["global", ".runtime", ".sessions", ".config"]);
-        const { readFindings } = await import("./data-access.js");
+        const { readFindings } = await import("../data/access.js");
         const projects = project
             ? [project]
             : fs.readdirSync(phrenPath, { withFileTypes: true })

package/mcp/dist/{cli-ops.js → cli/ops.js}

@@ -1,13 +1,13 @@
 import * as fs from "fs";
 import * as path from "path";
 import { execFileSync } from "child_process";
-import { EXEC_TIMEOUT_MS, findProjectNameCaseInsensitive, getPhrenPath, normalizeProjectNameForCreate, } from "./shared.js";
-import { isValidProjectName, errorMessage } from "./utils.js";
-import { readTasksAcrossProjects, TASKS_FILENAME } from "./data-access.js";
-import { applyGravity } from "./data-tasks.js";
-import { buildIndex, queryRows } from "./shared-index.js";
-import { resolveSubprocessArgs } from "./cli-hooks.js";
-import { listAllSessions, getSessionArtifacts } from "./mcp-session.js";
+import { EXEC_TIMEOUT_MS, findProjectNameCaseInsensitive, getPhrenPath, normalizeProjectNameForCreate, } from "../shared.js";
+import { isValidProjectName, errorMessage } from "../utils.js";
+import { readTasksAcrossProjects, TASKS_FILENAME } from "../data/access.js";
+import { applyGravity } from "../data/tasks.js";
+import { buildIndex, queryRows } from "../shared/index.js";
+import { resolveSubprocessArgs } from "./hooks.js";
+import { listAllSessions, getSessionArtifacts } from "../tools/session.js";
 export function handleTaskView(profile) {
     const docs = readTasksAcrossProjects(getPhrenPath(), profile);
     if (!docs.length) {
@@ -100,8 +100,8 @@ export function handleSessionsView(args) {
     console.log(`\n${sessions.length} session(s). Use \`phren sessions <id>\` to drill into one.`);
 }
 export async function handleQuickstart() {
-    const { runInit } = await import("./init.js");
-    const { runLink } = await import("./link.js");
+    const { runInit } = await import("../init/init.js");
+    const { runLink } = await import("../link/link.js");
     const dirBasename = path.basename(process.cwd());
     const readline = await import("readline");
     const rl = readline.createInterface({ input: process.stdin, output: process.stdout });

package/mcp/dist/{cli-search.js → cli/search.js}

@@ -1,9 +1,10 @@
 import * as fs from "fs";
 import * as path from "path";
-import { runtimeFile } from "./shared.js";
-import { buildIndex, extractSnippet, queryDocRows, queryRows, queryEntityLinks, queryDocBySourceKey, logEntityMiss } from "./shared-index.js";
-import { buildFtsQueryVariants, errorMessage, isValidProjectName } from "./utils.js";
-import { keywordFallbackSearch } from "./core-search.js";
+import { runtimeFile } from "../shared.js";
+import { buildIndex, extractSnippet, queryDocRows, queryRows, queryEntityLinks, queryDocBySourceKey, logEntityMiss } from "../shared/index.js";
+import { buildFtsQueryVariants, errorMessage, isValidProjectName } from "../utils.js";
+import { logger } from "../logger.js";
+import { keywordFallbackSearch } from "../core/search.js";
 const MAX_HISTORY = 20;
 const SEARCH_TYPE_ALIASES = {
     skills: "skill",
@@ -35,7 +36,7 @@ export function readSearchHistory(phrenPath) {
     }
     catch (err) {
         if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] readSearchHistory: ${errorMessage(err)}\n`);
+            logger.debug("cli-search", `readSearchHistory: ${errorMessage(err)}`);
         return [];
     }
 }
@@ -249,12 +250,12 @@ export async function runSearch(opts, phrenPath, profile) {
         if (!rows) {
             if (opts.query) {
                 try {
-                    const { logSearchMiss } = await import("./mcp-search.js");
+                    const { logSearchMiss } = await import("../tools/search.js");
                     logSearchMiss(phrenPath, opts.query, opts.project);
                 }
                 catch (err) {
                     if ((process.env.PHREN_DEBUG))
-                        process.stderr.write(`[phren] search logSearchMiss: ${errorMessage(err)}\n`);
+                        logger.debug("cli-search", `search logSearchMiss: ${errorMessage(err)}`);
                 }
             }
             const scope = [