@phren/cli 0.0.28 → 0.0.32

package/mcp/dist/{governance-scores.js → governance/scores.js}

@@ -1,9 +1,10 @@
 import * as crypto from "crypto";
 import * as fs from "fs";
 import * as path from "path";
-import { appendAuditLog, debugLog, isRecord, memoryScoresFile, memoryUsageLogFile, runtimeFile } from "./shared.js";
-import { withFileLock, isFiniteNumber, hasValidSchemaVersion } from "./shared-governance.js";
-import { errorMessage } from "./utils.js";
+import { appendAuditLog, debugLog, isRecord, memoryScoresFile, memoryUsageLogFile, runtimeFile } from "../shared.js";
+import { withFileLock, isFiniteNumber, hasValidSchemaVersion } from "../shared/governance.js";
+import { errorMessage } from "../utils.js";
+import { logger } from "../logger.js";
 const GOVERNANCE_SCHEMA_VERSION = 1;
 const DEFAULT_MEMORY_SCORES_FILE = {
     schemaVersion: GOVERNANCE_SCHEMA_VERSION,
@@ -114,8 +115,7 @@ function readScoreJournal(phrenPath) {
                 return JSON.parse(line);
             }
             catch (err) {
-                if ((process.env.PHREN_DEBUG))
-                    process.stderr.write(`[phren] readScoreJournal parseLine: ${errorMessage(err)}\n`);
+                logger.debug("scores", `readScoreJournal parseLine: ${errorMessage(err)}`);
                 return null;
             }
         })
@@ -147,8 +147,7 @@ function claimScoreJournal(phrenPath) {
                 return JSON.parse(line);
             }
             catch (err) {
-                if ((process.env.PHREN_DEBUG))
-                    process.stderr.write(`[phren] claimScoreJournal parseLine: ${errorMessage(err)}\n`);
+                logger.debug("scores", `claimScoreJournal parseLine: ${errorMessage(err)}`);
                 return null;
             }
         })
@@ -163,8 +162,7 @@ function claimScoreJournal(phrenPath) {
             fs.unlinkSync(claimedFile);
         }
         catch (err) {
-            if ((process.env.PHREN_DEBUG))
-                process.stderr.write(`[phren] claimScoreJournal unlinkClaim: ${errorMessage(err)}\n`);
+            logger.debug("scores", `claimScoreJournal unlinkClaim: ${errorMessage(err)}`);
         }
     }
 }
@@ -276,7 +274,7 @@ export function recordFeedback(phrenPath, key, feedback, sessionId) {
     appendAuditLog(phrenPath, "memory_feedback", `key=${key} feedback=${feedback}`);
     // When feedback is "helpful", mark correlated query entries for future boost
     if (feedback === "helpful" && sessionId) {
-        import("./query-correlation.js").then(({ markCorrelationsHelpful: markHelpful }) => {
+        import("../query-correlation.js").then(({ markCorrelationsHelpful: markHelpful }) => {
             const colonIdx = key.indexOf(":");
             const docKey = colonIdx >= 0 ? key.slice(0, colonIdx) : key;
             markHelpful(phrenPath, sessionId, docKey);

package/mcp/dist/hooks.js

@@ -9,6 +9,8 @@ import { EXEC_TIMEOUT_QUICK_MS, PhrenError, debugLog, runtimeFile, homePath, ins
 import { errorMessage } from "./utils.js";
 import { hookConfigPath } from "./provider-adapters.js";
 import { PACKAGE_SPEC } from "./package-metadata.js";
+import { logger } from "./logger.js";
+import { withFileLock } from "./shared/governance.js";
 export function commandExists(cmd) {
     try {
         const whichCmd = process.platform === "win32" ? "where.exe" : "which";
@@ -67,10 +69,6 @@ function phrenPackageSpec() {
 export function shellEscape(s) {
     return "'" + s.replace(/'/g, "'\\''") + "'";
 }
-/** @deprecated Use shellEscape instead */
-function shellSingleQuote(value) {
-    return shellEscape(value);
-}
 function buildPackageLifecycleCommands() {
     const packageSpec = phrenPackageSpec();
     return {
@@ -84,10 +82,10 @@ export function buildLifecycleCommands(phrenPath) {
     const entry = resolveCliEntryScript();
     const isWindows = process.platform === "win32";
     const escapedPhren = phrenPath.replace(/\\/g, "\\\\").replace(/"/g, '\\"');
-    const quotedPhren = shellSingleQuote(phrenPath);
+    const quotedPhren = shellEscape(phrenPath);
     if (entry) {
         const escapedEntry = entry.replace(/\\/g, "\\\\").replace(/"/g, '\\"');
-        const quotedEntry = shellSingleQuote(entry);
+        const quotedEntry = shellEscape(entry);
         if (isWindows) {
             return {
                 sessionStart: `set "PHREN_PATH=${escapedPhren}" && node "${escapedEntry}" hook-session-start`,
@@ -126,7 +124,7 @@ function withHookToolEnv(command, tool) {
     if (process.platform === "win32") {
         return `set "PHREN_HOOK_TOOL=${tool}" && ${command}`;
     }
-    return `PHREN_HOOK_TOOL=${shellSingleQuote(tool)} ${command}`;
+    return `PHREN_HOOK_TOOL=${shellEscape(tool)} ${command}`;
 }
 function withHookToolLifecycleCommands(lifecycle, tool) {
     return {
@@ -153,10 +151,10 @@ function installSessionWrapper(tool, phrenPath) {
     const content = `#!/bin/sh
 set -u
 
-REAL_BIN=${shellSingleQuote(realBinary)}
-DEFAULT_PHREN_PATH=${shellSingleQuote(phrenPath)}
+REAL_BIN=${shellEscape(realBinary)}
+DEFAULT_PHREN_PATH=${shellEscape(phrenPath)}
 PHREN_PATH="\${PHREN_PATH:-$DEFAULT_PHREN_PATH}"
-ENTRY_SCRIPT=${shellSingleQuote(entry || "")}
+ENTRY_SCRIPT=${shellEscape(entry || "")}
 export PHREN_HOOK_TOOL="${tool}"
 
 if [ ! -x "$REAL_BIN" ]; then
@@ -399,9 +397,7 @@ async function validateAndResolveWebhook(webhook) {
     }
     catch (err) {
         debugLog(`validateAndResolveWebhook lookup failed for ${parsed.hostname}: ${errorMessage(err)}`);
-        // DNS resolution failed; allow the fetch to proceed with the original URL
-        // (fetch will do its own resolution and may fail with a network error)
-        return { resolvedUrl: webhook, host: parsed.host };
+        return { error: `webhook hostname "${parsed.hostname}" could not be resolved: ${errorMessage(err)}` };
     }
 }
 const DEFAULT_CUSTOM_HOOK_TIMEOUT = 5000;
@@ -430,18 +426,24 @@ export function readCustomHooks(phrenPath) {
 function appendHookErrorLog(phrenPath, event, message) {
     const logPath = runtimeFile(phrenPath, "hook-errors.log");
     const line = `[${new Date().toISOString()}] [${event}] ${message}\n`;
-    fs.appendFileSync(logPath, line);
     try {
-        const stat = fs.statSync(logPath);
-        if (stat.size > 200_000) {
-            const content = fs.readFileSync(logPath, "utf-8");
-            const lines = content.split("\n").filter(Boolean);
-            atomicWriteText(logPath, lines.slice(-HOOK_ERROR_LOG_MAX_LINES).join("\n") + "\n");
-        }
+        withFileLock(logPath, () => {
+            fs.appendFileSync(logPath, line);
+            try {
+                const stat = fs.statSync(logPath);
+                if (stat.size > 200_000) {
+                    const content = fs.readFileSync(logPath, "utf-8");
+                    const lines = content.split("\n").filter(Boolean);
+                    atomicWriteText(logPath, lines.slice(-HOOK_ERROR_LOG_MAX_LINES).join("\n") + "\n");
+                }
+            }
+            catch (err) {
+                logger.debug("appendHookErrorLog rotate", errorMessage(err));
+            }
+        });
     }
     catch (err) {
-        if (process.env.PHREN_DEBUG)
-            process.stderr.write(`[phren] appendHookErrorLog rotate: ${errorMessage(err)}\n`);
+        logger.debug("appendHookErrorLog lock", errorMessage(err));
     }
 }
 export function runCustomHooks(phrenPath, event, env = {}) {
@@ -488,8 +490,7 @@ export function runCustomHooks(phrenPath, event, env = {}) {
                     appendHookErrorLog(phrenPath, event, message);
                 }
                 catch (logErr) {
-                    if (process.env.PHREN_DEBUG)
-                        process.stderr.write(`[phren] runCustomHooks webhookErrorLog: ${errorMessage(logErr)}\n`);
+                    logger.debug("runCustomHooks webhookErrorLog", errorMessage(logErr));
                 }
             });
             continue;
@@ -503,12 +504,22 @@ export function runCustomHooks(phrenPath, event, env = {}) {
             continue;
         }
         const shellArgs = isWindows ? ["/c", hook.command] : ["-c", hook.command];
+        // On Windows, cmd /c expands %VAR% in the command string.
+        // Sanitize env values to prevent shell metacharacter injection.
+        const mergedEnv = { ...process.env, PHREN_PATH: phrenPath, PHREN_HOOK_EVENT: event, ...env };
+        if (isWindows) {
+            for (const [key, val] of Object.entries(mergedEnv)) {
+                if (typeof val === "string") {
+                    mergedEnv[key] = val.replace(/[&|<>^%]/g, "");
+                }
+            }
+        }
         try {
             execFileSync(shellCmd, shellArgs, {
                 cwd: phrenPath,
                 encoding: "utf8",
                 timeout: hook.timeout ?? DEFAULT_CUSTOM_HOOK_TIMEOUT,
-                env: { ...process.env, PHREN_PATH: phrenPath, PHREN_HOOK_EVENT: event, ...env },
+                env: mergedEnv,
                 stdio: ["ignore", "ignore", "pipe"],
             });
         }
@@ -520,8 +531,7 @@ export function runCustomHooks(phrenPath, event, env = {}) {
                 appendHookErrorLog(phrenPath, event, errorMessage(err));
             }
             catch (logErr) {
-                if (process.env.PHREN_DEBUG)
-                    process.stderr.write(`[phren] runCustomHooks hookErrorLog: ${errorMessage(logErr)}\n`);
+                logger.debug("runCustomHooks hookErrorLog", errorMessage(logErr));
             }
         }
     }
@@ -572,8 +582,7 @@ export function configureAllHooks(phrenPath, options = {}) {
                 existing = JSON.parse(fs.readFileSync(cursorFile, "utf8"));
             }
             catch (err) {
-                if (process.env.PHREN_DEBUG)
-                    process.stderr.write(`[phren] configureAllHooks cursorRead: ${errorMessage(err)}\n`);
+                logger.debug("configureAllHooks cursorRead", errorMessage(err));
             }
             const config = {
                 ...existing,
@@ -604,8 +613,7 @@ export function configureAllHooks(phrenPath, options = {}) {
                 existing = JSON.parse(fs.readFileSync(codexFile, "utf8"));
             }
             catch (err) {
-                if (process.env.PHREN_DEBUG)
-                    process.stderr.write(`[phren] configureAllHooks codexRead: ${errorMessage(err)}\n`);
+                logger.debug("configureAllHooks codexRead", errorMessage(err));
             }
             const config = {
                 ...existing,

package/mcp/dist/index-query.js

@@ -1,5 +1,6 @@
 import * as path from "path";
 import { debugLog } from "./shared.js";
+import { logger } from "./logger.js";
 function describeSqlValue(value) {
     if (value === null)
         return "null";
@@ -78,7 +79,9 @@ export function queryRows(db, sql, params) {
         return results[0].values;
     }
     catch (err) {
-        debugLog(`queryRows failed: ${err instanceof Error ? err.message : "unknown error"}`);
+        const msg = err instanceof Error ? err.message : "unknown error";
+        logger.debug("queryRows", `DB query failed: ${msg}`);
+        debugLog(`queryRows failed: ${msg}`);
         return null;
     }
 }

package/mcp/dist/index.js

@@ -4,22 +4,22 @@ import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js"
 import * as fs from "fs";
 import * as path from "path";
 import { findPhrenPathWithArg, debugLog, runtimeDir, } from "./shared.js";
-import { log as structuredLog } from "./logger.js";
-import { buildIndex, updateFileInIndex as updateFileInIndexFn, } from "./shared-index.js";
+import { log as structuredLog, logger } from "./logger.js";
+import { buildIndex, updateFileInIndex as updateFileInIndexFn, } from "./shared/index.js";
 import { runCustomHooks } from "./hooks.js";
-import { register as registerSearch } from "./mcp-search.js";
-import { register as registerTask } from "./mcp-tasks.js";
-import { register as registerFinding } from "./mcp-finding.js";
-import { register as registerMemory } from "./mcp-memory.js";
-import { register as registerData } from "./mcp-data.js";
-import { register as registerGraph } from "./mcp-graph.js";
-import { register as registerSession } from "./mcp-session.js";
-import { register as registerOps } from "./mcp-ops.js";
-import { register as registerSkills } from "./mcp-skills.js";
-import { register as registerHooks } from "./mcp-hooks.js";
-import { register as registerExtract } from "./mcp-extract.js";
-import { register as registerConfig } from "./mcp-config.js";
-import { mcpResponse } from "./mcp-types.js";
+import { register as registerSearch } from "./tools/search.js";
+import { register as registerTask } from "./tools/tasks.js";
+import { register as registerFinding } from "./tools/finding.js";
+import { register as registerMemory } from "./tools/memory.js";
+import { register as registerData } from "./tools/data.js";
+import { register as registerGraph } from "./tools/graph.js";
+import { register as registerSession } from "./tools/session.js";
+import { register as registerOps } from "./tools/ops.js";
+import { register as registerSkills } from "./tools/skills.js";
+import { register as registerHooks } from "./tools/hooks.js";
+import { register as registerExtract } from "./tools/extract.js";
+import { register as registerConfig } from "./tools/config.js";
+import { mcpResponse } from "./tools/types.js";
 import { errorMessage } from "./utils.js";
 import { runTopLevelCommand } from "./entrypoint.js";
 import { startEmbeddingWarmup } from "./startup-embedding.js";
@@ -48,14 +48,12 @@ function cleanStaleLocks(phrenPath) {
                 }
             }
             catch (err) {
-                if ((process.env.PHREN_DEBUG))
-                    process.stderr.write(`[phren] cleanStaleLocks statFile: ${errorMessage(err)}\n`);
+                logger.warn("cleanStaleLocks", `statFile: ${errorMessage(err)}`);
             }
         }
     }
     catch (err) {
-        if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] cleanStaleLocks readdir: ${errorMessage(err)}\n`);
+        logger.warn("cleanStaleLocks", `readdir: ${errorMessage(err)}`);
     }
 }
 async function main() {
@@ -67,7 +65,7 @@ async function main() {
         db = await buildIndex(phrenPath, profile);
         indexReady = true;
         // Load embedding cache and kick off background embedding (fire-and-forget)
-        const { getEmbeddingCache } = await import("./shared-embedding-cache.js");
+        const { getEmbeddingCache } = await import("./shared/embedding-cache.js");
         const embCache = getEmbeddingCache(phrenPath);
         void startEmbeddingWarmup(db, embCache);
     }
@@ -83,21 +81,29 @@ async function main() {
     const WRITE_TIMEOUT_MS = 30_000;
     async function rebuildIndex() {
         runCustomHooks(phrenPath, "pre-index");
-        indexReady = false;
+        const oldDb = db;
         try {
-            db?.close();
+            indexReady = false;
+            db = await buildIndex(phrenPath, profile);
+            indexReady = true;
+            try {
+                oldDb?.close();
+            }
+            catch (err) {
+                logger.warn("rebuildIndex", `dbClose: ${errorMessage(err)}`);
+            }
         }
         catch (err) {
-            if ((process.env.PHREN_DEBUG))
-                process.stderr.write(`[phren] rebuildIndex dbClose: ${errorMessage(err)}\n`);
+            // Restore old state on failure
+            db = oldDb;
+            indexReady = !!oldDb;
+            throw err;
         }
-        db = await buildIndex(phrenPath, profile);
-        indexReady = true;
         runCustomHooks(phrenPath, "post-index");
     }
     async function withWriteQueue(fn) {
         if (writeQueueDepth >= MAX_QUEUE_DEPTH) {
-            throw new Error(`Write queue full (${MAX_QUEUE_DEPTH} items). Try again shortly.`);
+            return mcpResponse({ ok: false, error: `Write queue full (${MAX_QUEUE_DEPTH} items). Try again shortly.`, errorCode: "TIMEOUT" });
         }
         writeQueueDepth++;
         const run = writeQueue.then(async () => {
@@ -158,8 +164,7 @@ async function main() {
                 trackToolCall(phrenPath, registeredName);
             }
             catch (err) {
-                if ((process.env.PHREN_DEBUG))
-                    process.stderr.write(`[phren] trackToolCall: ${errorMessage(err)}\n`);
+                logger.warn("trackToolCall", errorMessage(err));
             }
             return handler(...args);
         };
@@ -197,6 +202,25 @@ async function main() {
     const transport = new StdioServerTransport();
     await server.connect(transport);
     console.error(`phren-mcp running (${phrenPath})`);
+    // Graceful shutdown: drain write queue and close DB before exit
+    async function shutdown(signal) {
+        structuredLog("info", "shutdown", `Received ${signal}, draining write queue...`);
+        try {
+            await writeQueue;
+        }
+        catch {
+            // Write queue errors already logged
+        }
+        try {
+            db?.close();
+        }
+        catch (err) {
+            logger.warn("shutdown", `dbClose: ${errorMessage(err)}`);
+        }
+        process.exit(0);
+    }
+    process.on("SIGTERM", () => void shutdown("SIGTERM"));
+    process.on("SIGINT", () => void shutdown("SIGINT"));
 }
 if (!handledTopLevelCommand) {
     main().catch((err) => {

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

@@ -4,12 +4,12 @@
  */
 import * as fs from "fs";
 import * as path from "path";
-import { buildLifecycleCommands, commandExists } from "./hooks.js";
-import { isRecord, hookConfigPath, homePath, readRootManifest, atomicWriteText, } from "./shared.js";
-import { isFeatureEnabled, errorMessage } from "./utils.js";
-import { probeVsCodeConfig, resolveCodexMcpConfig, resolveCopilotMcpConfig, resolveCursorMcpConfig, } from "./provider-adapters.js";
-import { getMcpEnabledPreference, getHooksEnabledPreference } from "./init-preferences.js";
-import { resolveEntryScript, log, VERSION } from "./init-shared.js";
+import { buildLifecycleCommands, commandExists } from "../hooks.js";
+import { isRecord, hookConfigPath, homePath, readRootManifest, atomicWriteText, } from "../shared.js";
+import { isFeatureEnabled, errorMessage } from "../utils.js";
+import { probeVsCodeConfig, resolveCodexMcpConfig, resolveCopilotMcpConfig, resolveCursorMcpConfig, } from "../provider-adapters.js";
+import { getMcpEnabledPreference, getHooksEnabledPreference } from "./preferences.js";
+import { resolveEntryScript, log, VERSION } from "./shared.js";
 function getObjectProp(value, key) {
     const candidate = value[key];
     return isRecord(candidate) ? candidate : undefined;

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

@@ -6,24 +6,25 @@ import * as fs from "fs";
 import * as path from "path";
 import * as crypto from "crypto";
 import { execFileSync, spawnSync } from "child_process";
-import { configureAllHooks } from "./hooks.js";
-import { getMachineName, machineFilePath, persistMachineName } from "./machine-identity.js";
-import { atomicWriteText, debugLog, isRecord, hookConfigPath, homeDir, homePath, expandHomePath, findPhrenPath, getProjectDirs, readRootManifest, writeRootManifest, } from "./shared.js";
-import { isValidProjectName, errorMessage } from "./utils.js";
-import { codexJsonCandidates, copilotMcpCandidates, cursorMcpCandidates, vscodeMcpCandidates, } from "./provider-adapters.js";
-export { configureClaude, configureVSCode, configureCursorMcp, configureCopilotMcp, configureCodexMcp, logMcpTargetStatus, resetVSCodeProbeCache, patchJsonFile, } from "./init-config.js";
-export { getMcpEnabledPreference, setMcpEnabledPreference, getHooksEnabledPreference, setHooksEnabledPreference, } from "./init-preferences.js";
-export { PROJECT_OWNERSHIP_MODES, parseProjectOwnershipMode, getProjectOwnershipDefault, } from "./project-config.js";
-export { PROACTIVITY_LEVELS, getProactivityLevel, getProactivityLevelForFindings, getProactivityLevelForTask, } from "./proactivity.js";
-export { ensureGovernanceFiles, repairPreexistingInstall, runPostInitVerify, getVerifyOutcomeNote, listTemplates, detectProjectDir, isProjectTracked, ensureLocalGitRepo, resolvePreferredHomeDir, inferInitScaffoldFromRepo, } from "./init-setup.js";
+import { configureAllHooks } from "../hooks.js";
+import { getMachineName, machineFilePath, persistMachineName } from "../machine-identity.js";
+import { atomicWriteText, debugLog, isRecord, hookConfigPath, homeDir, homePath, expandHomePath, findPhrenPath, getProjectDirs, readRootManifest, writeRootManifest, } from "../shared.js";
+import { isValidProjectName, errorMessage } from "../utils.js";
+import { codexJsonCandidates, copilotMcpCandidates, cursorMcpCandidates, vscodeMcpCandidates, } from "../provider-adapters.js";
+import { logger } from "../logger.js";
+export { configureClaude, configureVSCode, configureCursorMcp, configureCopilotMcp, configureCodexMcp, logMcpTargetStatus, resetVSCodeProbeCache, patchJsonFile, } from "./config.js";
+export { getMcpEnabledPreference, setMcpEnabledPreference, getHooksEnabledPreference, setHooksEnabledPreference, } from "./preferences.js";
+export { PROJECT_OWNERSHIP_MODES, parseProjectOwnershipMode, getProjectOwnershipDefault, } from "../project-config.js";
+export { PROACTIVITY_LEVELS, getProactivityLevel, getProactivityLevelForFindings, getProactivityLevelForTask, } from "../proactivity.js";
+export { ensureGovernanceFiles, repairPreexistingInstall, runPostInitVerify, getVerifyOutcomeNote, listTemplates, detectProjectDir, isProjectTracked, ensureLocalGitRepo, resolvePreferredHomeDir, inferInitScaffoldFromRepo, } from "./setup.js";
 // Imports from helpers (used internally in this file)
-import { configureClaude, configureVSCode, configureCursorMcp, configureCopilotMcp, configureCodexMcp, logMcpTargetStatus, removeMcpServerAtPath, removeTomlMcpServer, isPhrenCommand, patchJsonFile, } from "./init-config.js";
-import { getMcpEnabledPreference, getHooksEnabledPreference, setMcpEnabledPreference, setHooksEnabledPreference, writeInstallPreferences, writeGovernanceInstallPreferences, readInstallPreferences, } from "./init-preferences.js";
-import { ensureGovernanceFiles, repairPreexistingInstall, runPostInitVerify, applyStarterTemplateUpdates, listTemplates, applyTemplate, ensureProjectScaffold, ensureLocalGitRepo, bootstrapFromExisting, ensureGitignoreEntry, upsertProjectEnvVar, updateMachinesYaml, detectProjectDir, isProjectTracked, inferInitScaffoldFromRepo, } from "./init-setup.js";
-import { DEFAULT_PHREN_PATH, STARTER_DIR, VERSION, log, confirmPrompt } from "./init-shared.js";
-import { PROJECT_OWNERSHIP_MODES, getProjectOwnershipDefault, } from "./project-config.js";
-import { getWorkflowPolicy, updateWorkflowPolicy } from "./shared-governance.js";
-import { addProjectToProfile } from "./profile-store.js";
+import { configureClaude, configureVSCode, configureCursorMcp, configureCopilotMcp, configureCodexMcp, logMcpTargetStatus, removeMcpServerAtPath, removeTomlMcpServer, isPhrenCommand, patchJsonFile, } from "./config.js";
+import { getMcpEnabledPreference, getHooksEnabledPreference, setMcpEnabledPreference, setHooksEnabledPreference, writeInstallPreferences, writeGovernanceInstallPreferences, readInstallPreferences, } from "./preferences.js";
+import { ensureGovernanceFiles, repairPreexistingInstall, runPostInitVerify, applyStarterTemplateUpdates, listTemplates, applyTemplate, ensureProjectScaffold, ensureLocalGitRepo, bootstrapFromExisting, ensureGitignoreEntry, upsertProjectEnvVar, updateMachinesYaml, detectProjectDir, isProjectTracked, inferInitScaffoldFromRepo, } from "./setup.js";
+import { DEFAULT_PHREN_PATH, STARTER_DIR, VERSION, log, confirmPrompt } from "./shared.js";
+import { PROJECT_OWNERSHIP_MODES, getProjectOwnershipDefault, } from "../project-config.js";
+import { getWorkflowPolicy, updateWorkflowPolicy } from "../shared/governance.js";
+import { addProjectToProfile } from "../profile-store.js";
 const PHREN_NPM_PACKAGE_NAME = "@phren/cli";
 function parseVersion(version) {
     const match = version.trim().match(/^(\d+)\.(\d+)\.(\d+)(?:-(.+))?/);
@@ -289,7 +290,7 @@ async function runWalkthrough(phrenPath) {
             log(style.success(`✓ ${item}`));
         }
     };
-    const { renderPhrenArt } = await import("./phren-art.js");
+    const { renderPhrenArt } = await import("../phren-art.js");
     log("");
     log(renderPhrenArt("  "));
     log("");
@@ -434,7 +435,7 @@ async function runWalkthrough(phrenPath) {
     log("  Change later: set PHREN_OLLAMA_URL=off to disable");
     let ollamaEnabled = false;
     try {
-        const { checkOllamaAvailable, checkModelAvailable, getOllamaUrl } = await import("./shared-ollama.js");
+        const { checkOllamaAvailable, checkModelAvailable, getOllamaUrl } = await import("../shared/ollama.js");
         if (getOllamaUrl()) {
             const ollamaUp = await checkOllamaAvailable();
             if (ollamaUp) {
@@ -463,8 +464,7 @@ async function runWalkthrough(phrenPath) {
         }
     }
     catch (err) {
-        if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] init ollamaCheck: ${errorMessage(err)}\n`);
+        logger.debug("init", `init ollamaCheck: ${errorMessage(err)}`);
     }
     printSection("Auto-Capture (Optional)");
     log("After each session, phren scans the conversation for insight-signal phrases");
@@ -663,7 +663,7 @@ async function runWalkthrough(phrenPath) {
     };
 }
 export async function warmSemanticSearch(phrenPath, profile) {
-    const { checkOllamaAvailable, checkModelAvailable, getOllamaUrl, getEmbeddingModel } = await import("./shared-ollama.js");
+    const { checkOllamaAvailable, checkModelAvailable, getOllamaUrl, getEmbeddingModel } = await import("../shared/ollama.js");
     const ollamaUrl = getOllamaUrl();
     if (!ollamaUrl)
         return "Semantic search: disabled.";
@@ -674,10 +674,10 @@ export async function warmSemanticSearch(phrenPath, profile) {
     if (!await checkModelAvailable()) {
         return `Semantic search not warmed: model ${model} is not pulled yet.`;
     }
-    const { buildIndex, listIndexedDocumentPaths } = await import("./shared-index.js");
-    const { getEmbeddingCache, formatEmbeddingCoverage } = await import("./shared-embedding-cache.js");
-    const { backgroundEmbedMissingDocs } = await import("./startup-embedding.js");
-    const { getPersistentVectorIndex } = await import("./shared-vector-index.js");
+    const { buildIndex, listIndexedDocumentPaths } = await import("../shared/index.js");
+    const { getEmbeddingCache, formatEmbeddingCoverage } = await import("../shared/embedding-cache.js");
+    const { backgroundEmbedMissingDocs } = await import("../startup-embedding.js");
+    const { getPersistentVectorIndex } = await import("../shared/vector-index.js");
     const db = await buildIndex(phrenPath, profile);
     try {
         const cache = getEmbeddingCache(phrenPath);
@@ -1450,7 +1450,7 @@ export async function runInit(opts = {}) {
     const walkthroughCoveredOllama = Boolean(process.env._PHREN_WALKTHROUGH_OLLAMA_SKIP) || (!hasExistingInstall && !opts.yes);
     if (!walkthroughCoveredOllama) {
         try {
-            const { checkOllamaAvailable, checkModelAvailable, getOllamaUrl } = await import("./shared-ollama.js");
+            const { checkOllamaAvailable, checkModelAvailable, getOllamaUrl } = await import("../shared/ollama.js");
             if (getOllamaUrl()) {
                 const ollamaUp = await checkOllamaAvailable();
                 if (ollamaUp) {
@@ -1471,8 +1471,7 @@ export async function runInit(opts = {}) {
             }
         }
         catch (err) {
-            if ((process.env.PHREN_DEBUG))
-                process.stderr.write(`[phren] init ollamaInstallHint: ${errorMessage(err)}\n`);
+            logger.debug("init", `init ollamaInstallHint: ${errorMessage(err)}`);
         }
     }
     for (const envLabel of writeWalkthroughEnvDefaults(phrenPath, opts)) {

package/mcp/dist/{init-preferences.js → init/preferences.js}

@@ -4,9 +4,9 @@
 import * as fs from "fs";
 import * as path from "path";
 import * as crypto from "crypto";
-import { debugLog, installPreferencesFile } from "./phren-paths.js";
-import { errorMessage } from "./utils.js";
-import { withFileLock } from "./shared-governance.js";
+import { debugLog, installPreferencesFile } from "../phren-paths.js";
+import { errorMessage } from "../utils.js";
+import { withFileLock } from "../shared/governance.js";
 function preferencesFile(phrenPath) {
     return installPreferencesFile(phrenPath);
 }

package/mcp/dist/{init-setup.js → init/setup.js}

@@ -5,19 +5,20 @@ import * as fs from "fs";
 import * as path from "path";
 import * as os from "os";
 import * as yaml from "js-yaml";
-import { atomicWriteText, debugLog, findProjectNameCaseInsensitive, hookConfigPath, EXEC_TIMEOUT_QUICK_MS, readRootManifest, sessionsDir, runtimeHealthFile, isRecord, } from "./shared.js";
-import { addProjectToProfile, listProfiles, resolveActiveProfile, setMachineProfile } from "./profile-store.js";
-import { getMachineName } from "./machine-identity.js";
+import { atomicWriteText, debugLog, findProjectNameCaseInsensitive, hookConfigPath, EXEC_TIMEOUT_QUICK_MS, readRootManifest, sessionsDir, runtimeHealthFile, isRecord, } from "../shared.js";
+import { addProjectToProfile, listProfiles, resolveActiveProfile, setMachineProfile } from "../profile-store.js";
+import { getMachineName } from "../machine-identity.js";
 import { execFileSync } from "child_process";
-import { GOVERNANCE_SCHEMA_VERSION, } from "./shared-governance.js";
-import { STOP_WORDS, errorMessage } from "./utils.js";
-import { ROOT, STARTER_DIR, VERSION, resolveEntryScript, commandVersion, versionAtLeast, nearestWritableTarget } from "./init-shared.js";
-import { readInstallPreferences } from "./init-preferences.js";
-import { TASKS_FILENAME } from "./data-tasks.js";
-import { getProjectOwnershipDefault, parseProjectOwnershipMode, readProjectConfig, writeProjectConfig, } from "./project-config.js";
-import { getBuiltinTopicConfig, normalizeBuiltinTopicDomain } from "./project-topics.js";
-import { writeSkillMd } from "./link-skills.js";
-import { syncScopeSkillsToDir } from "./skill-files.js";
+import { GOVERNANCE_SCHEMA_VERSION, } from "../shared/governance.js";
+import { STOP_WORDS, errorMessage } from "../utils.js";
+import { ROOT, STARTER_DIR, VERSION, resolveEntryScript, commandVersion, versionAtLeast, nearestWritableTarget } from "./shared.js";
+import { readInstallPreferences } from "./preferences.js";
+import { TASKS_FILENAME } from "../data/tasks.js";
+import { getProjectOwnershipDefault, parseProjectOwnershipMode, readProjectConfig, writeProjectConfig, } from "../project-config.js";
+import { getBuiltinTopicConfig, normalizeBuiltinTopicDomain } from "../project-topics.js";
+import { writeSkillMd } from "../link/skills.js";
+import { syncScopeSkillsToDir } from "../skill/files.js";
+import { logger } from "../logger.js";
 const LEGACY_SAMPLE_PROJECTS = new Set(["my-api", "my-frontend"]);
 function normalizeProjects(raw) {
     if (!Array.isArray(raw))
@@ -1052,16 +1053,14 @@ export function updateMachinesYaml(phrenPath, machine, profile) {
         }
     }
     catch (err) {
-        if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] updateMachinesYaml parse: ${errorMessage(err)}\n`);
+        logger.debug("setup", `updateMachinesYaml parse: ${errorMessage(err)}`);
     }
     // Passive init/link refreshes should keep an existing mapping; explicit overrides can remap.
     if (hasExistingMapping && !machine && !profile)
         return;
     const mapping = setMachineProfile(phrenPath, machineName, profileName);
-    if (!mapping.ok && (process.env.PHREN_DEBUG)) {
-        process.stderr.write(`[phren] updateMachinesYaml setMachineProfile: ${mapping.error}\n`);
-    }
+    if (!mapping.ok)
+        logger.debug("setup", `updateMachinesYaml setMachineProfile: ${mapping.error}`);
 }
 /**
  * Detect if a directory looks like a project that should be bootstrapped.
@@ -1262,8 +1261,7 @@ export function runPostInitVerify(phrenPath) {
         ftsOk = entries.some(d => d.isDirectory() && !d.name.startsWith("."));
     }
     catch (err) {
-        if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] runPostInitVerify projectScan: ${errorMessage(err)}\n`);
+        logger.debug("setup", `runPostInitVerify projectScan: ${errorMessage(err)}`);
         ftsOk = false;
     }
     checks.push({

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

@@ -5,9 +5,9 @@
 import * as fs from "fs";
 import * as path from "path";
 import { execFileSync } from "child_process";
-import { homePath, EXEC_TIMEOUT_QUICK_MS, debugLog } from "./shared.js";
-import { errorMessage } from "./utils.js";
-import { ROOT as PACKAGE_ROOT, VERSION } from "./package-metadata.js";
+import { homePath, EXEC_TIMEOUT_QUICK_MS, debugLog } from "../shared.js";
+import { errorMessage } from "../utils.js";
+import { ROOT as PACKAGE_ROOT, VERSION } from "../package-metadata.js";
 export const ROOT = PACKAGE_ROOT;
 export { VERSION };
 export const STARTER_DIR = path.join(ROOT, "starter");