@phren/cli 0.0.28 → 0.0.33

package/mcp/dist/capabilities/cli.js

@@ -32,11 +32,8 @@ export const cliManifest = {
         "graph.visualize": { implemented: false, reason: "Graph visualization is VS Code / web only" },
         "graph.link_findings": { implemented: true, handler: "cli-graph.ts:handleGraphLink" },
         // Config
-        "config.proactivity": { implemented: true, handler: "cli-config.ts:handleProactivity" },
-        "config.task_mode": { implemented: true, handler: "cli-config.ts:handleConfigTaskMode" },
-        "config.retention": { implemented: true, handler: "cli-config.ts:handleRetentionPolicy" },
-        "config.workflow": { implemented: true, handler: "cli-config.ts:handleWorkflowPolicy" },
-        "config.index": { implemented: true, handler: "cli-config.ts:handleIndexPolicy" },
+        "config.get": { implemented: true, handler: "cli-config.ts:handleConfigGet (per-domain)" },
+        "config.set": { implemented: true, handler: "cli-config.ts:handleConfigSet (proactivity, taskMode, findingSensitivity, retention, workflow, index)" },
         // Health / Sync / Session
         "health.check": { implemented: true, handler: "cli-actions.ts:handleDoctor" },
         "health.doctor_fix": { implemented: true, handler: "cli-actions.ts:handleDoctor --fix" },

package/mcp/dist/capabilities/mcp.js

@@ -14,8 +14,8 @@ export const mcpManifest = {
         "task.remove": { implemented: true, handler: "index.ts:remove_task" },
         "task.update": { implemented: true, handler: "index.ts:update_task" },
         "task.list": { implemented: true, handler: "index.ts:get_tasks" },
-        "task.pin": { implemented: true, handler: "index.ts:pin_task" },
-        "task.github_link": { implemented: true, handler: "index.ts:link_task_issue, promote_task_to_issue" },
+        "task.pin": { implemented: true, handler: "index.ts:update_task (pin)" },
+        "task.github_link": { implemented: true, handler: "index.ts:update_task (github_issue/github_url)" },
         // Hook management
         "hook.list": { implemented: true, handler: "index.ts:list_hooks" },
         "hook.toggle": { implemented: true, handler: "index.ts:toggle_hooks" },
@@ -32,11 +32,8 @@ export const mcpManifest = {
         "graph.visualize": { implemented: false, reason: "MCP returns data only; visualization is client-side" },
         "graph.link_findings": { implemented: true, handler: "index.ts:link_findings" },
         // Config
-        "config.proactivity": { implemented: true, handler: "index.ts:get_config, set_proactivity" },
-        "config.task_mode": { implemented: true, handler: "index.ts:get_config, set_task_mode" },
-        "config.retention": { implemented: true, handler: "index.ts:get_config, set_retention_policy" },
-        "config.workflow": { implemented: true, handler: "index.ts:get_config, set_workflow_policy, set_finding_sensitivity" },
-        "config.index": { implemented: true, handler: "index.ts:get_config, set_index_policy" },
+        "config.get": { implemented: true, handler: "index.ts:get_config (supports all domains including topic)" },
+        "config.set": { implemented: true, handler: "index.ts:set_config (proactivity, taskMode, findingSensitivity, retention, workflow, index, topic)" },
         // Health / Sync / Session
         "health.check": { implemented: true, handler: "index.ts:health_check" },
         "health.doctor_fix": { implemented: true, handler: "index.ts:doctor_fix" },
@@ -46,7 +43,7 @@ export const mcpManifest = {
         // Skill management
         "skill.list": { implemented: true, handler: "index.ts:list_skills" },
         "skill.read": { implemented: true, handler: "index.ts:read_skill" },
-        "skill.enable": { implemented: true, handler: "index.ts:enable_skill, disable_skill" },
+        "skill.enable": { implemented: true, handler: "index.ts:toggle_skill" },
         "skill.write": { implemented: true, handler: "index.ts:write_skill" },
         // Project management
         "project.list": { implemented: true, handler: "index.ts:list_projects" },

package/mcp/dist/capabilities/types.js

@@ -29,11 +29,8 @@ export const ACTION_KEYS = [
     "graph.visualize",
     "graph.link_findings",
     // Config
-    "config.proactivity",
-    "config.task_mode",
-    "config.retention",
-    "config.workflow",
-    "config.index",
+    "config.get",
+    "config.set",
     // Health / Sync / Session
     "health.check",
     "health.doctor_fix",

package/mcp/dist/capabilities/vscode.js

@@ -32,11 +32,8 @@ export const vscodeManifest = {
         "graph.visualize": { implemented: true, handler: "graphWebview.ts:showGraphWebview (webview panel)" },
         "graph.link_findings": { implemented: false, reason: "Link findings is MCP-only" },
         // Config
-        "config.proactivity": { implemented: false, reason: "Config tools are CLI-only" },
-        "config.task_mode": { implemented: false, reason: "Config tools are CLI-only" },
-        "config.retention": { implemented: false, reason: "Config tools are CLI-only" },
-        "config.workflow": { implemented: false, reason: "Config tools are CLI-only" },
-        "config.index": { implemented: false, reason: "Config tools are CLI-only" },
+        "config.get": { implemented: false, reason: "Config tools are CLI-only" },
+        "config.set": { implemented: false, reason: "Config tools are CLI-only" },
         // Health / Sync / Session
         "health.check": { implemented: true, handler: "extension.ts:phren.doctor" },
         "health.doctor_fix": { implemented: true, handler: "extension.ts:phren.doctorFix" },

package/mcp/dist/capabilities/web-ui.js

@@ -32,11 +32,8 @@ export const webUiManifest = {
         "graph.visualize": { implemented: true, handler: "memory-ui-graph-app.ts:graph tab (Sigma.js v3 + ForceAtlas2)" },
         "graph.link_findings": { implemented: false, reason: "No link findings action in web UI" },
         // Config
-        "config.proactivity": { implemented: false, reason: "Config is CLI-only" },
-        "config.task_mode": { implemented: true, handler: "memory-ui-server.ts:/api/settings (workflow policy)" },
-        "config.retention": { implemented: false, reason: "Config is CLI-only" },
-        "config.workflow": { implemented: true, handler: "memory-ui-server.ts:/api/settings (workflow policy)" },
-        "config.index": { implemented: false, reason: "Config is CLI-only" },
+        "config.get": { implemented: true, handler: "memory-ui-server.ts:/api/settings (read)" },
+        "config.set": { implemented: true, handler: "memory-ui-server.ts:/api/settings (workflow policy, task mode)" },
         // Health / Sync / Session
         "health.check": { implemented: true, handler: "memory-ui-server.ts:/api/runtime-health" },
         "health.doctor_fix": { implemented: false, reason: "Doctor --fix is CLI-only" },

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

@@ -1,19 +1,20 @@
 import * as fs from "fs";
 import * as path from "path";
-import { runtimeFile, getPhrenPath, getProjectDirs } from "./shared.js";
-import { recordFeedback, flushEntryScores, getWorkflowPolicy, } from "./shared-governance.js";
-import { upsertCanonical } from "./shared-content.js";
-import { errorMessage, isValidProjectName } from "./utils.js";
-import { addFinding as addFindingCore } from "./core-finding.js";
-import { runDoctor } from "./link.js";
-import { startWebUi } from "./memory-ui.js";
-import { startShell } from "./shell.js";
-import { runPhrenUpdate } from "./update.js";
-import { readRuntimeHealth, readReviewQueue, readReviewQueueAcrossProjects } from "./data-access.js";
-import { runSearch, runFragmentSearch, parseFragmentSearchArgs, runRelatedDocs, parseRelatedDocsArgs } from "./cli-search.js";
-import { resolveRuntimeProfile } from "./runtime-profile.js";
-import { getProjectConsolidationStatus, CONSOLIDATION_ENTRY_THRESHOLD } from "./content-validate.js";
-import { listAllSessions } from "./mcp-session.js";
+import { runtimeFile, getPhrenPath, getProjectDirs } from "../shared.js";
+import { recordFeedback, flushEntryScores, getWorkflowPolicy, } from "../shared/governance.js";
+import { upsertCanonical } from "../shared/content.js";
+import { errorMessage, isValidProjectName } from "../utils.js";
+import { logger } from "../logger.js";
+import { addFinding as addFindingCore } from "../core/finding.js";
+import { runDoctor } from "../link/link.js";
+import { startWebUi } from "../ui/memory-ui.js";
+import { startShell } from "../shell/shell.js";
+import { runPhrenUpdate } from "../update.js";
+import { readRuntimeHealth, readReviewQueue, readReviewQueueAcrossProjects } from "../data/access.js";
+import { runSearch, runFragmentSearch, parseFragmentSearchArgs, runRelatedDocs, parseRelatedDocsArgs } from "./search.js";
+import { resolveRuntimeProfile } from "../runtime-profile.js";
+import { getProjectConsolidationStatus, CONSOLIDATION_ENTRY_THRESHOLD } from "../content/validate.js";
+import { listAllSessions } from "../tools/session.js";
 async function runAndPrint(fn) {
     const result = await fn();
     if (result.lines.length > 0)
@@ -69,7 +70,7 @@ export async function handleDoctor(args) {
     const agentsOnly = args.includes("--agents");
     const parityCheck = args.includes("--parity");
     if (parityCheck) {
-        const { ALL_MANIFESTS, ACTION_KEYS } = await import("./capabilities/index.js");
+        const { ALL_MANIFESTS, ACTION_KEYS } = await import("../capabilities/index.js");
         const gaps = [];
         for (const key of ACTION_KEYS) {
             for (const manifest of ALL_MANIFESTS) {
@@ -157,7 +158,7 @@ export async function handleDoctor(args) {
                     }
                     catch (err) {
                         if ((process.env.PHREN_DEBUG))
-                            process.stderr.write(`[phren] doctor searchMissParse: ${errorMessage(err)}\n`);
+                            logger.debug("cli-actions", `doctor searchMissParse: ${errorMessage(err)}`);
                     }
                 }
                 const topMisses = [...tokenCounts.entries()]
@@ -174,7 +175,7 @@ export async function handleDoctor(args) {
     }
     catch (err) {
         if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] doctor searchMissAnalysis: ${errorMessage(err)}\n`);
+            logger.debug("cli-actions", `doctor searchMissAnalysis: ${errorMessage(err)}`);
     }
     const semStatus = await getSemanticSearchStatus(getPhrenPath(), profile || undefined);
     if (!semStatus.ollamaUrl) {
@@ -193,9 +194,9 @@ export async function handleDoctor(args) {
 }
 async function getSemanticSearchStatus(phrenPath, profile) {
     try {
-        const { checkOllamaAvailable, checkModelAvailable, getOllamaUrl, getEmbeddingModel } = await import("./shared-ollama.js");
-        const { getEmbeddingCache, formatEmbeddingCoverage } = await import("./shared-embedding-cache.js");
-        const { listIndexedDocumentPaths } = await import("./shared-index.js");
+        const { checkOllamaAvailable, checkModelAvailable, getOllamaUrl, getEmbeddingModel } = await import("../shared/ollama.js");
+        const { getEmbeddingCache, formatEmbeddingCoverage } = await import("../shared/embedding-cache.js");
+        const { listIndexedDocumentPaths } = await import("../shared/index.js");
         const ollamaUrl = getOllamaUrl();
         if (!ollamaUrl)
             return { ollamaUrl: null };
@@ -213,7 +214,7 @@ async function getSemanticSearchStatus(phrenPath, profile) {
     }
     catch (err) {
         if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] getSemanticSearchStatus: ${errorMessage(err)}\n`);
+            logger.debug("cli-actions", `getSemanticSearchStatus: ${errorMessage(err)}`);
         return { ollamaUrl: null, status: "error", error: errorMessage(err) };
     }
 }
@@ -289,6 +290,9 @@ export async function handleUpdate(args) {
     if (!result.ok) {
         process.exitCode = 1;
     }
+    else {
+        console.log("Run 'npx phren init' to refresh hooks and config.");
+    }
 }
 export async function handleReview(args) {
     const phrenPath = getPhrenPath();

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

@@ -1,17 +1,17 @@
-import { getPhrenPath } from "./shared.js";
+import { getPhrenPath } from "../shared.js";
 // Re-export from split modules so existing test imports keep working
-export { detectTaskIntent, parseHookInput, applyTrustFilter, rankResults, selectSnippets, buildHookOutput, trackSessionMetrics, filterTaskByPriority, parseCitations, validateCitation, annotateStale, getProjectGlobBoost, clearProjectGlobCache, clearCitationValidCache, filterConversationInsightsForProactivity, extractToolFindings, filterToolFindingsForProactivity, } from "./cli-hooks.js";
-export { scoreFindingCandidate } from "./cli-extract.js";
-import { handleHookPrompt, handleHookSessionStart, handleHookStop, handleBackgroundSync, handleHookContext, handleHookTool, } from "./cli-hooks.js";
-import { handleExtractMemories } from "./cli-extract.js";
-import { handleGovernMemories, handlePruneMemories, handleConsolidateMemories, handleMaintain, handleBackgroundMaintenance, } from "./cli-govern.js";
-import { handleConfig, handleIndexPolicy, handleRetentionPolicy, handleWorkflowPolicy, } from "./cli-config.js";
-import { parseSearchArgs } from "./cli-search.js";
-import { handleDetectSkills, handleFindingNamespace, handleHooksNamespace, handleProjectsNamespace, handleSkillsNamespace, handleSkillList, handleTaskNamespace, } from "./cli-namespaces.js";
-import { handleTaskView, handleSessionsView, handleQuickstart, handleDebugInjection, handleInspectIndex, } from "./cli-ops.js";
-import { handleAddFinding, handleDoctor, handleFragmentSearch, handleMemoryUi, handlePinCanonical, handleQualityFeedback, handleRelatedDocs, handleReview, handleConsolidationStatus, handleSessionContext, handleSearch, handleShell, handleStatus, handleUpdate, } from "./cli-actions.js";
-import { handleGraphNamespace } from "./cli-graph.js";
-import { resolveRuntimeProfile } from "./runtime-profile.js";
+export { detectTaskIntent, parseHookInput, applyTrustFilter, rankResults, selectSnippets, buildHookOutput, trackSessionMetrics, filterTaskByPriority, parseCitations, validateCitation, annotateStale, getProjectGlobBoost, clearProjectGlobCache, clearCitationValidCache, filterConversationInsightsForProactivity, extractToolFindings, filterToolFindingsForProactivity, } from "./hooks.js";
+export { scoreFindingCandidate } from "./extract.js";
+import { handleHookPrompt, handleHookSessionStart, handleHookStop, handleBackgroundSync, handleHookContext, handleHookTool, } from "./hooks.js";
+import { handleExtractMemories } from "./extract.js";
+import { handleGovernMemories, handlePruneMemories, handleConsolidateMemories, handleMaintain, handleBackgroundMaintenance, } from "./govern.js";
+import { handleConfig, handleIndexPolicy, handleRetentionPolicy, handleWorkflowPolicy, } from "./config.js";
+import { parseSearchArgs } from "./search.js";
+import { handleDetectSkills, handleFindingNamespace, handleHooksNamespace, handleProjectsNamespace, handleSkillsNamespace, handleSkillList, handleTaskNamespace, } from "./namespaces.js";
+import { handleTaskView, handleSessionsView, handleQuickstart, handleDebugInjection, handleInspectIndex, } from "./ops.js";
+import { handleAddFinding, handleDoctor, handleFragmentSearch, handleMemoryUi, handlePinCanonical, handleQualityFeedback, handleRelatedDocs, handleReview, handleConsolidationStatus, handleSessionContext, handleSearch, handleShell, handleStatus, handleUpdate, } from "./actions.js";
+import { handleGraphNamespace } from "./graph.js";
+import { resolveRuntimeProfile } from "../runtime-profile.js";
 // ── CLI router ───────────────────────────────────────────────────────────────
 export async function runCliCommand(command, args) {
     const getProfile = () => resolveRuntimeProfile(getPhrenPath());

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

@@ -1,14 +1,14 @@
-import { getPhrenPath, readRootManifest } from "./shared.js";
-import { installPreferencesFile } from "./phren-paths.js";
-import { getIndexPolicy, updateIndexPolicy, getRetentionPolicy, updateRetentionPolicy, getWorkflowPolicy, updateWorkflowPolicy, mergeConfig, VALID_TASK_MODES, VALID_FINDING_SENSITIVITY, } from "./shared-governance.js";
-import { listMachines as listMachinesStore, listProfiles as listProfilesStore, listProfiles } from "./data-access.js";
-import { setTelemetryEnabled, getTelemetrySummary, resetTelemetry } from "./telemetry.js";
-import { governanceInstallPreferencesFile, readInstallPreferences, readGovernanceInstallPreferences, writeInstallPreferences, writeGovernanceInstallPreferences, } from "./init-preferences.js";
-import { PROACTIVITY_LEVELS, getProactivityLevel, getProactivityLevelForTask, getProactivityLevelForFindings, } from "./proactivity.js";
-import { PROJECT_OWNERSHIP_MODES, getProjectOwnershipDefault, parseProjectOwnershipMode, updateProjectConfigOverrides, } from "./project-config.js";
-import { isValidProjectName, learnedSynonymsPath, learnSynonym, loadLearnedSynonyms, removeLearnedSynonym, } from "./utils.js";
+import { getPhrenPath, readRootManifest } from "../shared.js";
+import { installPreferencesFile } from "../phren-paths.js";
+import { getIndexPolicy, updateIndexPolicy, getRetentionPolicy, updateRetentionPolicy, getWorkflowPolicy, updateWorkflowPolicy, mergeConfig, VALID_TASK_MODES, VALID_FINDING_SENSITIVITY, } from "../shared/governance.js";
+import { listMachines as listMachinesStore, listProfiles as listProfilesStore, listProfiles } from "../data/access.js";
+import { setTelemetryEnabled, getTelemetrySummary, resetTelemetry } from "../telemetry.js";
+import { governanceInstallPreferencesFile, readInstallPreferences, readGovernanceInstallPreferences, writeInstallPreferences, writeGovernanceInstallPreferences, } from "../init/preferences.js";
+import { PROACTIVITY_LEVELS, getProactivityLevel, getProactivityLevelForTask, getProactivityLevelForFindings, } from "../proactivity.js";
+import { PROJECT_OWNERSHIP_MODES, getProjectOwnershipDefault, parseProjectOwnershipMode, updateProjectConfigOverrides, } from "../project-config.js";
+import { isValidProjectName, learnedSynonymsPath, learnSynonym, loadLearnedSynonyms, removeLearnedSynonym, } from "../utils.js";
 // ── Shared helpers ────────────────────────────────────────────────────────────
-export function parseProjectArg(args) {
+function parseProjectArg(args) {
     const project = args.find((a) => a.startsWith("--project="))?.slice("--project=".length)
         ?? (args.indexOf("--project") !== -1 ? args[args.indexOf("--project") + 1] : undefined);
     const rest = args.filter((a, i) => a !== "--project" && !a.startsWith("--project=") && args[i - 1] !== "--project");
@@ -53,7 +53,7 @@ function formatConfigAsTable(label, rows) {
         console.log(`  ${k.padEnd(maxKey)}  ${v}`);
     }
 }
-export function handleConfigShow(args) {
+function handleConfigShow(args) {
     const phrenPath = getPhrenPath();
     const { project: projectArg } = parseProjectArg(args);
     if (projectArg) {
@@ -461,7 +461,7 @@ function handleConfigFindingSensitivity(args) {
 // ── LLM config ───────────────────────────────────────────────────────────────
 const EXPENSIVE_MODEL_RE = /opus|sonnet|gpt-4(?!o-mini)/i;
 const DEFAULT_LLM_MODEL = "gpt-4o-mini / claude-haiku-4-5-20251001";
-export function printSemanticCostNotice(model) {
+function printSemanticCostNotice(model) {
     const effectiveModel = model || process.env.PHREN_LLM_MODEL || DEFAULT_LLM_MODEL;
     console.log(`  Note: Each semantic check is ~80 input + ~5 output tokens (one call per 'maybe' pair, cached 24h).`);
     console.log(`  Current model: ${effectiveModel}`);

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

@@ -1,16 +1,16 @@
-import { debugLog, appendAuditLog, EXEC_TIMEOUT_MS, getPhrenPath, } from "./shared.js";
-import { appendReviewQueue, getRetentionPolicy, recordFeedback, flushEntryScores, entryScoreKey, } from "./shared-governance.js";
-import { detectProject } from "./shared-index.js";
-import { commandExists } from "./hooks.js";
-import { runGit as runGitShared, isFeatureEnabled, clampInt, errorMessage, resolveExecCommand } from "./utils.js";
-import { appendFindingJournal, compactFindingJournals } from "./finding-journal.js";
-import { getProactivityLevelForTask, getProactivityLevelForFindings, shouldAutoCaptureFindingsForLevel } from "./proactivity.js";
+import { debugLog, appendAuditLog, EXEC_TIMEOUT_MS, getPhrenPath, } from "../shared.js";
+import { appendReviewQueue, getRetentionPolicy, recordFeedback, flushEntryScores, entryScoreKey, } from "../shared/governance.js";
+import { detectProject } from "../shared/index.js";
+import { commandExists } from "../hooks.js";
+import { runGit as runGitShared, isFeatureEnabled, clampInt, errorMessage, resolveExecCommand } from "../utils.js";
+import { appendFindingJournal, compactFindingJournals } from "../finding/journal.js";
+import { getProactivityLevelForTask, getProactivityLevelForFindings, shouldAutoCaptureFindingsForLevel } from "../proactivity.js";
 import * as fs from "fs";
 import * as os from "os";
 import * as path from "path";
 import * as crypto from "crypto";
 import { execFileSync } from "child_process";
-import { resolveRuntimeProfile } from "./runtime-profile.js";
+import { resolveRuntimeProfile } from "../runtime-profile.js";
 function runGit(cwd, args) {
     return runGitShared(cwd, args, EXEC_TIMEOUT_MS, debugLog);
 }

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

@@ -1,12 +1,13 @@
-import { appendAuditLog, qualityMarkers, getProjectDirs, getPhrenPath, } from "./shared.js";
-import { appendReviewQueue, getRetentionPolicy, consolidateProjectFindings, updateRuntimeHealth, pruneDeadMemories, } from "./shared-governance.js";
-import { filterTrustedFindingsDetailed, } from "./shared-content.js";
+import { appendAuditLog, qualityMarkers, getProjectDirs, getPhrenPath, } from "../shared.js";
+import { appendReviewQueue, getRetentionPolicy, consolidateProjectFindings, updateRuntimeHealth, pruneDeadMemories, } from "../shared/governance.js";
+import { filterTrustedFindingsDetailed, } from "../shared/content.js";
 import * as fs from "fs";
 import * as path from "path";
-import { handleExtractMemories } from "./cli-extract.js";
-import { errorMessage } from "./utils.js";
-import { compactFindingJournals } from "./finding-journal.js";
-import { resolveRuntimeProfile } from "./runtime-profile.js";
+import { handleExtractMemories } from "./extract.js";
+import { errorMessage } from "../utils.js";
+import { logger } from "../logger.js";
+import { compactFindingJournals } from "../finding/journal.js";
+import { resolveRuntimeProfile } from "../runtime-profile.js";
 // ── Shared helpers ───────────────────────────────────────────────────────────
 function targetProjects(projectArg) {
     const profile = resolveRuntimeProfile(getPhrenPath());
@@ -145,7 +146,7 @@ export async function handlePruneMemories(args = []) {
         }
         catch (err) {
             if ((process.env.PHREN_DEBUG))
-                process.stderr.write(`[phren] cli-govern retrievalLog readParse: ${errorMessage(err)}\n`);
+                logger.debug("cli-govern", `retrievalLog readParse: ${errorMessage(err)}`);
         }
     }
     // Build map of last retrieval date by file+bullet key
@@ -227,10 +228,10 @@ export async function handleConsolidateMemories(args = []) {
         return;
     console.log(`Updated backups (${backups.length}): ${backups.join(", ")}`);
 }
-export async function handleGcMaintain(args = []) {
+async function handleGcMaintain(args = []) {
     const dryRun = args.includes("--dry-run");
     const phrenPath = getPhrenPath();
-    const { execSync } = await import("child_process");
+    const { execFileSync } = await import("child_process");
     const report = {
         gitGcRan: false,
         commitsSquashed: 0,
@@ -243,7 +244,7 @@ export async function handleGcMaintain(args = []) {
     }
     else {
         try {
-            execSync("git gc --aggressive --quiet", { cwd: phrenPath, stdio: "pipe" });
+            execFileSync("git", ["gc", "--aggressive", "--quiet"], { cwd: phrenPath, stdio: "pipe" });
             report.gitGcRan = true;
             console.log("git gc --aggressive: done");
         }
@@ -255,7 +256,10 @@ export async function handleGcMaintain(args = []) {
     const sevenDaysAgo = new Date(Date.now() - 7 * 86400000).toISOString().slice(0, 10);
     let oldCommits = [];
     try {
-        const raw = execSync(`git log --before="${sevenDaysAgo}" --format="%H %ci %s"`, { cwd: phrenPath, encoding: "utf8" }).trim();
+        const raw = execFileSync("git", ["log", `--before=${sevenDaysAgo}`, "--format=%H %ci %s"], {
+            cwd: phrenPath,
+            encoding: "utf8",
+        }).trim();
         if (raw) {
             oldCommits = raw.split("\n").filter((l) => l.includes("auto-save:") || l.includes("[auto]"));
         }
@@ -294,8 +298,11 @@ export async function handleGcMaintain(args = []) {
             try {
                 const oldest = hashes[hashes.length - 1];
                 const newest = hashes[0];
-                // Use git rebase --onto to squash: squash all into the oldest parent
-                const parentOfOldest = execSync(`git rev-parse ${oldest}^`, { cwd: phrenPath, encoding: "utf8" }).trim();
+                // Use git rev-parse to get the parent of the oldest commit
+                const parentOfOldest = execFileSync("git", ["rev-parse", `${oldest}^`], {
+                    cwd: phrenPath,
+                    encoding: "utf8",
+                }).trim();
                 // Build rebase script via env variable to squash all but first to "squash"
                 const rebaseScript = hashes
                     .map((h, i) => `${i === hashes.length - 1 ? "pick" : "squash"} ${h} auto-save`)
@@ -303,8 +310,12 @@ export async function handleGcMaintain(args = []) {
                     .join("\n");
                 const scriptPath = path.join(phrenPath, ".runtime", `gc-rebase-${weekKey}.sh`);
                 fs.writeFileSync(scriptPath, rebaseScript);
-                // Use GIT_SEQUENCE_EDITOR to feed our script
-                execSync(`GIT_SEQUENCE_EDITOR="cat ${scriptPath} >" git rebase -i ${parentOfOldest}`, { cwd: phrenPath, stdio: "pipe" });
+                // Use GIT_SEQUENCE_EDITOR env var to feed our script to git rebase
+                execFileSync("git", ["rebase", "-i", parentOfOldest], {
+                    cwd: phrenPath,
+                    stdio: "pipe",
+                    env: { ...process.env, GIT_SEQUENCE_EDITOR: `cat ${scriptPath} >` },
+                });
                 fs.unlinkSync(scriptPath);
                 report.commitsSquashed += hashes.length - 1;
                 console.log(`Squashed ${hashes.length} auto-save commits for week of ${weekKey} (${newest.slice(0, 7)}..${oldest.slice(0, 7)}).`);
@@ -502,7 +513,7 @@ export async function handleBackgroundMaintenance(projectArg) {
         }
         catch (err) {
             if ((process.env.PHREN_DEBUG))
-                process.stderr.write(`[phren] cli-govern backgroundMaintenance unlockFinal: ${errorMessage(err)}\n`);
+                logger.debug("cli-govern", `backgroundMaintenance unlockFinal: ${errorMessage(err)}`);
         }
     }
 }

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

@@ -1,7 +1,8 @@
-import { getPhrenPath } from "./shared.js";
-import { buildIndex, queryRows } from "./shared-index.js";
-import { resolveRuntimeProfile } from "./runtime-profile.js";
-import { isValidProjectName, errorMessage } from "./utils.js";
+import { getPhrenPath } from "../shared.js";
+import { buildIndex, queryRows } from "../shared/index.js";
+import { resolveRuntimeProfile } from "../runtime-profile.js";
+import { isValidProjectName, errorMessage } from "../utils.js";
+import { logger } from "../logger.js";
 /**
  * CLI: phren graph [--project <name>] [--limit <n>]
  * Displays the fragment knowledge graph as a table.
@@ -105,7 +106,7 @@ export async function handleGraphLink(args) {
     }
     catch (err) {
         if (process.env.PHREN_DEBUG)
-            process.stderr.write(`[phren] graph link insert fragment: ${errorMessage(err)}\n`);
+            logger.debug("cli-graph", `graph link insert fragment: ${errorMessage(err)}`);
     }
     const fragmentResult = db.exec("SELECT id FROM entities WHERE name = ? AND type = ?", [normalizedFragment, "fragment"]);
     if (!fragmentResult?.length || !fragmentResult[0]?.values?.length) {
@@ -118,7 +119,7 @@ export async function handleGraphLink(args) {
     }
     catch (err) {
         if (process.env.PHREN_DEBUG)
-            process.stderr.write(`[phren] graph link insert document: ${errorMessage(err)}\n`);
+            logger.debug("cli-graph", `graph link insert document: ${errorMessage(err)}`);
     }
     const docResult = db.exec("SELECT id FROM entities WHERE name = ? AND type = ?", [sourceDoc, "document"]);
     if (!docResult?.length || !docResult[0]?.values?.length) {
@@ -134,10 +135,10 @@ export async function handleGraphLink(args) {
         process.exit(1);
     }
     // Persist to manual-links.json
-    const { runtimeFile } = await import("./shared.js");
+    const { runtimeFile } = await import("../shared.js");
     const fs = await import("fs");
     const crypto = await import("crypto");
-    const { withFileLock } = await import("./shared-governance.js");
+    const { withFileLock } = await import("../shared/governance.js");
     const manualLinksPath = runtimeFile(phrenPath, "manual-links.json");
     try {
         withFileLock(manualLinksPath, () => {
@@ -147,7 +148,7 @@ export async function handleGraphLink(args) {
                     existing = JSON.parse(fs.readFileSync(manualLinksPath, "utf8"));
                 }
                 catch (err) {
-                    process.stderr.write(`[phren] link_fragment: manual-links.json is malformed — aborting to avoid data loss: ${err instanceof Error ? err.message : String(err)}\n`);
+                    logger.error("cli-graph", `link_fragment: manual-links.json is malformed — aborting to avoid data loss: ${err instanceof Error ? err.message : String(err)}`);
                     throw err;
                 }
             }

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

@@ -1,5 +1,5 @@
-import { parseCitationComment, validateFindingCitation, } from "./content-citation.js";
-import { capCache } from "./shared.js";
+import { parseCitationComment, validateFindingCitation, } from "../content/citation.js";
+import { capCache } from "../shared.js";
 // ── Citation validation ──────────────────────────────────────────────────────
 const citationValidCache = new Map();
 export function clearCitationValidCache() {

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

@@ -1,13 +1,13 @@
 // cli-hooks-context.ts — HookContext: everything a hook handler needs as plain data + helpers.
 // Centralizes the "resolve state and check guards" pattern so hook handlers don't
 // reach into governance, init, project-config, hooks, init-setup, etc. directly.
-import { getPhrenPath, readRootManifest, appendAuditLog, } from "./shared.js";
-import { updateRuntimeHealth, } from "./shared-governance.js";
-import { detectProject } from "./shared-index.js";
-import { getHooksEnabledPreference } from "./init.js";
-import { isToolHookEnabled } from "./hooks.js";
-import { isProjectHookEnabled } from "./project-config.js";
-import { resolveRuntimeProfile } from "./runtime-profile.js";
+import { getPhrenPath, readRootManifest, appendAuditLog, } from "../shared.js";
+import { updateRuntimeHealth, } from "../shared/governance.js";
+import { detectProject } from "../shared/index.js";
+import { getHooksEnabledPreference } from "../init/init.js";
+import { isToolHookEnabled } from "../hooks.js";
+import { isProjectHookEnabled } from "../project-config.js";
+import { resolveRuntimeProfile } from "../runtime-profile.js";
 /** Build a HookContext from the current process environment. */
 export function buildHookContext() {
     const phrenPath = getPhrenPath();
@@ -38,19 +38,19 @@ export function handleGuardSkip(ctx, hookName, reason, healthUpdate) {
     appendAuditLog(ctx.phrenPath, hookName, `status=${reason}`);
 }
 // Re-export frequently used functions so hook handlers can import from one place
-export { debugLog, appendAuditLog, getPhrenPath, readRootManifest, sessionMarker, runtimeFile, EXEC_TIMEOUT_MS, getProjectDirs, findProjectNameCaseInsensitive, homePath, } from "./shared.js";
-export { updateRuntimeHealth, getWorkflowPolicy, withFileLock, appendReviewQueue, recordFeedback, getQualityMultiplier, } from "./shared-governance.js";
-export { detectProject } from "./shared-index.js";
-export { isProjectHookEnabled, readProjectConfig, getProjectSourcePath } from "./project-config.js";
-export { resolveRuntimeProfile } from "./runtime-profile.js";
-export { detectProjectDir, ensureLocalGitRepo, isProjectTracked, repairPreexistingInstall, } from "./init-setup.js";
-export { getProactivityLevelForTask, getProactivityLevelForFindings } from "./proactivity.js";
-export { hasExplicitFindingSignal, shouldAutoCaptureFindingsForLevel } from "./proactivity.js";
-export { FINDING_SENSITIVITY_CONFIG } from "./cli-config.js";
-export { isFeatureEnabled, errorMessage } from "./utils.js";
-export { bootstrapPhrenDotEnv } from "./phren-dotenv.js";
-export { finalizeTaskSession } from "./task-lifecycle.js";
-export { appendFindingJournal } from "./finding-journal.js";
-export { getHooksEnabledPreference } from "./init.js";
-export { isToolHookEnabled } from "./hooks.js";
-export { runDoctor } from "./link.js";
+export { debugLog, appendAuditLog, getPhrenPath, readRootManifest, sessionMarker, runtimeFile, EXEC_TIMEOUT_MS, getProjectDirs, findProjectNameCaseInsensitive, homePath, } from "../shared.js";
+export { updateRuntimeHealth, buildSyncStatus, getWorkflowPolicy, withFileLock, appendReviewQueue, recordFeedback, getQualityMultiplier, } from "../shared/governance.js";
+export { detectProject } from "../shared/index.js";
+export { isProjectHookEnabled, readProjectConfig, getProjectSourcePath } from "../project-config.js";
+export { resolveRuntimeProfile } from "../runtime-profile.js";
+export { detectProjectDir, ensureLocalGitRepo, isProjectTracked, repairPreexistingInstall, } from "../init/setup.js";
+export { getProactivityLevelForTask, getProactivityLevelForFindings } from "../proactivity.js";
+export { hasExplicitFindingSignal, shouldAutoCaptureFindingsForLevel } from "../proactivity.js";
+export { FINDING_SENSITIVITY_CONFIG } from "./config.js";
+export { isFeatureEnabled, errorMessage } from "../utils.js";
+export { bootstrapPhrenDotEnv } from "../phren-dotenv.js";
+export { finalizeTaskSession } from "../task/lifecycle.js";
+export { appendFindingJournal } from "../finding/journal.js";
+export { getHooksEnabledPreference } from "../init/init.js";
+export { isToolHookEnabled } from "../hooks.js";
+export { runDoctor } from "../link/link.js";

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

@@ -1,7 +1,8 @@
 import * as fs from "fs";
 import * as path from "path";
-import { capCache } from "./shared.js";
-import { errorMessage } from "./utils.js";
+import { capCache } from "../shared.js";
+import { errorMessage } from "../utils.js";
+import { logger } from "../logger.js";
 // ── Glob matching and project frontmatter ────────────────────────────────────
 const projectGlobCache = new Map();
 export function clearProjectGlobCache() {
@@ -45,8 +46,7 @@ function parseProjectGlobs(phrenPathLocal, project) {
         }
     }
     catch (err) {
-        if (process.env.PHREN_DEBUG)
-            process.stderr.write(`[phren] getProjectGlobs: ${errorMessage(err)}\n`);
+        logger.debug("hooks-globs", `getProjectGlobs: ${errorMessage(err)}`);
     }
     projectGlobCache.set(project, globs);
     capCache(projectGlobCache);

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

@@ -1,9 +1,10 @@
-import { recordInjection, recordRetrieval, } from "./shared-governance.js";
-import { getDocSourceKey, } from "./shared-index.js";
-import { logImpact, extractFindingIdsFromSnippet, } from "./finding-impact.js";
-import { isFeatureEnabled, errorMessage } from "./utils.js";
-import { annotateStale } from "./cli-hooks-citations.js";
-import { approximateTokens, fileRelevanceBoost, branchMatchBoost } from "./shared-retrieval.js";
+import { recordInjection, recordRetrieval, } from "../shared/governance.js";
+import { getDocSourceKey, } from "../shared/index.js";
+import { logImpact, extractFindingIdsFromSnippet, } from "../finding/impact.js";
+import { isFeatureEnabled, errorMessage } from "../utils.js";
+import { annotateStale } from "./hooks-citations.js";
+import { approximateTokens, fileRelevanceBoost, branchMatchBoost } from "../shared/retrieval.js";
+import { logger } from "../logger.js";
 // ── Progressive disclosure helpers ────────────────────────────────────────────
 function buildOneLiner(snippet) {
     const lines = snippet.split("\n").map(l => l.trim()).filter(l => l.length > 0);
@@ -55,8 +56,7 @@ export function buildHookOutput(selected, usedTokens, intent, gitCtx, detectedPr
                 recordRetrieval(phrenPathLocal, `${injected.doc.project}/${injected.doc.filename}`, injected.doc.type);
             }
             catch (err) {
-                if (process.env.PHREN_DEBUG)
-                    process.stderr.write(`[phren] injectContext recordRetrieval: ${errorMessage(err)}\n`);
+                logger.debug("hooks-output", `injectContext recordRetrieval: ${errorMessage(err)}`);
             }
         }
     }
@@ -107,8 +107,7 @@ export function buildHookOutput(selected, usedTokens, intent, gitCtx, detectedPr
                 recordRetrieval(phrenPathLocal, doc.path ?? doc.filename, doc.type);
             }
             catch (err) {
-                if (process.env.PHREN_DEBUG)
-                    process.stderr.write(`[phren] injectContext recordRetrievalOrdered: ${errorMessage(err)}\n`);
+                logger.debug("hooks-output", `injectContext recordRetrievalOrdered: ${errorMessage(err)}`);
             }
             parts.push(`[${getDocSourceKey(doc, phrenPathLocal)}] (${doc.type})`);
             parts.push(annotateStale(snippet));