@phren/cli 0.0.28 → 0.0.33

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() {
@@ -67,14 +65,14 @@ 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);
     }
     catch (error) {
         const msg = error instanceof Error ? error.message : String(error);
         structuredLog("error", "startup", `Failed to build phren index: ${msg}`);
-        console.error("Failed to build phren index at startup:", error);
+        console.error("Failed to build phren index at startup:", msg);
         process.exit(1);
     }
     let writeQueue = Promise.resolve();
@@ -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("");
@@ -434,37 +435,31 @@ 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");
-        if (getOllamaUrl()) {
-            const ollamaUp = await checkOllamaAvailable();
-            if (ollamaUp) {
-                const modelReady = await checkModelAvailable();
-                if (modelReady) {
-                    log("  Ollama detected with nomic-embed-text ready.");
-                    ollamaEnabled = await prompts.confirm("Enable semantic search for fuzzy/paraphrase recovery?", false);
-                }
-                else {
-                    log("  Ollama detected, but nomic-embed-text is not pulled yet.");
-                    ollamaEnabled = await prompts.confirm("Enable semantic search for fuzzy/paraphrase recovery? (will pull nomic-embed-text)", false);
-                    if (ollamaEnabled) {
-                        log("  Run after init: ollama pull nomic-embed-text");
-                    }
-                }
+        const { checkOllamaStatus } = await import("../shared/ollama.js");
+        const status = await checkOllamaStatus();
+        if (status === "ready") {
+            log("  Ollama detected with nomic-embed-text ready.");
+            ollamaEnabled = await prompts.confirm("Enable semantic search for fuzzy/paraphrase recovery?", false);
+        }
+        else if (status === "no_model") {
+            log("  Ollama detected, but nomic-embed-text is not pulled yet.");
+            ollamaEnabled = await prompts.confirm("Enable semantic search for fuzzy/paraphrase recovery? (will pull nomic-embed-text)", false);
+            if (ollamaEnabled) {
+                log("  Run after init: ollama pull nomic-embed-text");
             }
-            else {
-                log("  Ollama not detected. Install it to enable semantic search:");
-                log("    https://ollama.com  →  then: ollama pull nomic-embed-text");
-                ollamaEnabled = await prompts.confirm("Enable semantic search (Ollama not installed yet)?", false);
-                if (ollamaEnabled) {
-                    log(style.success("  Semantic search enabled — will activate once Ollama is running."));
-                    log("  To disable: set PHREN_OLLAMA_URL=off in your shell profile");
-                }
+        }
+        else if (status === "not_running") {
+            log("  Ollama not detected. Install it to enable semantic search:");
+            log("    https://ollama.com  →  then: ollama pull nomic-embed-text");
+            ollamaEnabled = await prompts.confirm("Enable semantic search (Ollama not installed yet)?", false);
+            if (ollamaEnabled) {
+                log(style.success("  Semantic search enabled — will activate once Ollama is running."));
+                log("  To disable: set PHREN_OLLAMA_URL=off in your shell profile");
             }
         }
     }
     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 +658,7 @@ 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 +669,10 @@ 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);
@@ -1450,29 +1445,23 @@ 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");
-            if (getOllamaUrl()) {
-                const ollamaUp = await checkOllamaAvailable();
-                if (ollamaUp) {
-                    const modelReady = await checkModelAvailable();
-                    if (modelReady) {
-                        log("\n  Semantic search: Ollama + nomic-embed-text ready.");
-                    }
-                    else {
-                        log("\n  Semantic search: Ollama running, but nomic-embed-text not pulled.");
-                        log("  Run: ollama pull nomic-embed-text");
-                    }
-                }
-                else {
-                    log("\n  Tip: Install Ollama for semantic search (optional).");
-                    log("  https://ollama.com → then: ollama pull nomic-embed-text");
-                    log("  (Set PHREN_OLLAMA_URL=off to hide this message)");
-                }
+            const { checkOllamaStatus } = await import("../shared/ollama.js");
+            const status = await checkOllamaStatus();
+            if (status === "ready") {
+                log("\n  Semantic search: Ollama + nomic-embed-text ready.");
+            }
+            else if (status === "no_model") {
+                log("\n  Semantic search: Ollama running, but nomic-embed-text not pulled.");
+                log("  Run: ollama pull nomic-embed-text");
+            }
+            else if (status === "not_running") {
+                log("\n  Tip: Install Ollama for semantic search (optional).");
+                log("  https://ollama.com → then: ollama pull nomic-embed-text");
+                log("  (Set PHREN_OLLAMA_URL=off to hide this message)");
             }
         }
         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)) {
@@ -2004,6 +1993,28 @@ export async function runUninstall(opts = {}) {
     catch (err) {
         debugLog(`uninstall: cleanup failed for ${contextFile}: ${errorMessage(err)}`);
     }
+    // Remove global CLAUDE.md symlink (created by linkGlobal -> ~/.claude/CLAUDE.md)
+    const globalClaudeLink = homePath(".claude", "CLAUDE.md");
+    try {
+        if (fs.lstatSync(globalClaudeLink).isSymbolicLink()) {
+            fs.unlinkSync(globalClaudeLink);
+            log(`  Removed global CLAUDE.md symlink (${globalClaudeLink})`);
+        }
+    }
+    catch {
+        // Does not exist or not a symlink — nothing to do
+    }
+    // Remove copilot-instructions.md symlink (created by linkGlobal -> ~/.github/copilot-instructions.md)
+    const copilotInstrLink = homePath(".github", "copilot-instructions.md");
+    try {
+        if (fs.lstatSync(copilotInstrLink).isSymbolicLink()) {
+            fs.unlinkSync(copilotInstrLink);
+            log(`  Removed copilot-instructions.md symlink (${copilotInstrLink})`);
+        }
+    }
+    catch {
+        // Does not exist or not a symlink — nothing to do
+    }
     // Sweep agent skill directories for symlinks pointing into the phren store
     if (phrenPath) {
         try {

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");
@@ -33,7 +33,7 @@ export function commandVersion(cmd, args = ["--version"]) {
         return null;
     }
 }
-export function parseSemverTriple(raw) {
+function parseSemverTriple(raw) {
     const match = raw.match(/(\d+)\.(\d+)\.(\d+)/);
     if (!match)
         return null;

package/mcp/dist/init-bootstrap.js

@@ -0,0 +1,21 @@
+/**
+ * Bootstrap-current-project prompting and execution for init.
+ */
+import { debugLog } from "./shared.js";
+import { bootstrapFromExisting, } from "./init/setup.js";
+import { log } from "./init/shared.js";
+/**
+ * Bootstrap a project from an existing directory into phren.
+ */
+export function bootstrapProject(phrenPath, projectPath, profile, ownership, label) {
+    try {
+        const created = bootstrapFromExisting(phrenPath, projectPath, {
+            profile,
+            ownership,
+        });
+        log(`\n${label} "${created.project}" (${created.ownership})`);
+    }
+    catch (e) {
+        debugLog(`Bootstrap from CWD failed: ${e instanceof Error ? e.message : String(e)}`);
+    }
+}

package/mcp/dist/init-detect.js

@@ -0,0 +1,38 @@
+/**
+ * Detection helpers for init: bootstrap target, install markers, path resolution.
+ */
+import * as fs from "fs";
+import * as path from "path";
+import { expandHomePath } from "./shared.js";
+import { detectProjectDir, isProjectTracked } from "./init/setup.js";
+import { DEFAULT_PHREN_PATH } from "./init/shared.js";
+export function normalizedBootstrapProjectName(projectPath) {
+    return path.basename(projectPath).toLowerCase().replace(/[^a-z0-9_-]/g, "-");
+}
+export function getPendingBootstrapTarget(phrenPath, _opts) {
+    const cwdProject = detectProjectDir(process.cwd(), phrenPath);
+    if (!cwdProject)
+        return null;
+    const projectName = normalizedBootstrapProjectName(cwdProject);
+    if (isProjectTracked(phrenPath, projectName))
+        return null;
+    return { path: cwdProject, mode: "detected" };
+}
+export function hasInstallMarkers(phrenPath) {
+    // Require at least two markers to consider this a real install.
+    // A partial clone or failed init may create one directory but not finish.
+    if (!fs.existsSync(phrenPath))
+        return false;
+    let found = 0;
+    if (fs.existsSync(path.join(phrenPath, "machines.yaml")))
+        found++;
+    if (fs.existsSync(path.join(phrenPath, ".config")))
+        found++;
+    if (fs.existsSync(path.join(phrenPath, "global")))
+        found++;
+    return found >= 2;
+}
+export function resolveInitPhrenPath(opts) {
+    const raw = opts._walkthroughStoragePath || process.env.PHREN_PATH || DEFAULT_PHREN_PATH;
+    return path.resolve(expandHomePath(raw));
+}