@phren/cli 0.0.28 → 0.0.33

package/mcp/dist/{shell-view.js → shell/view.js}

@@ -4,16 +4,17 @@
  */
 import * as fs from "fs";
 import * as path from "path";
-import { canonicalTaskFilePath, listProjectCards, readTasks, readFindings, readReviewQueue, readRuntimeHealth, resolveTaskFilePath, } from "./data-access.js";
-import { style, badge, separator, stripAnsi, truncateLine, renderWidth, wrapSegments, lineViewport, shellHelpText, gradient, } from "./shell-render.js";
-import { formatSelectableLine, viewportWithStatus, } from "./shell-view-list.js";
-import { SUB_VIEWS, TAB_ICONS, } from "./shell-types.js";
-import { tasksByFilter, queueByFilter, } from "./shell-palette.js";
-import { listMachines, listProfiles, } from "./data-access.js";
-import { readInstallPreferences } from "./init-preferences.js";
-import { isProjectHookEnabled, readProjectConfig } from "./project-config.js";
-import { getScopedSkills } from "./skill-registry.js";
-import { errorMessage } from "./utils.js";
+import { canonicalTaskFilePath, listProjectCards, readTasks, readFindings, readReviewQueue, readRuntimeHealth, resolveTaskFilePath, } from "../data/access.js";
+import { style, badge, separator, stripAnsi, truncateLine, renderWidth, wrapSegments, lineViewport, shellHelpText, gradient, } from "./render.js";
+import { formatSelectableLine, viewportWithStatus, } from "./view-list.js";
+import { SUB_VIEWS, TAB_ICONS, } from "./types.js";
+import { tasksByFilter, queueByFilter, } from "./palette.js";
+import { listMachines, listProfiles, } from "../data/access.js";
+import { readInstallPreferences } from "../init/preferences.js";
+import { isProjectHookEnabled, readProjectConfig } from "../project-config.js";
+import { getScopedSkills } from "../skill/registry.js";
+import { errorMessage } from "../utils.js";
+import { logger } from "../logger.js";
 // ── Tab bar ────────────────────────────────────────────────────────────────
 function renderTabBar(state) {
     const cols = renderWidth();
@@ -249,8 +250,7 @@ function parseSubsections(taskPath, project, cache) {
         }
     }
     catch (err) {
-        if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] buildSubsectionMap: ${errorMessage(err)}\n`);
+        logger.debug("shell-view", `buildSubsectionMap: ${errorMessage(err)}`);
     }
     const newCache = { project, map };
     return { map, cache: newCache };
@@ -564,7 +564,7 @@ function renderHooksView(ctx, cursor, height) {
     ctx.setScroll(vp.scrollStart);
     return vp.lines;
 }
-export { writeInstallPreferences } from "./init-preferences.js";
+export { writeInstallPreferences } from "../init/preferences.js";
 // ── Machines/Profiles view ─────────────────────────────────────────────────
 function renderMachinesView(phrenPath) {
     const machines = listMachines(phrenPath);

package/mcp/dist/{skill-files.js → skill/files.js}

@@ -1,11 +1,12 @@
 import * as fs from "fs";
 import * as path from "path";
-import { homePath } from "./shared.js";
-import { findProjectDir } from "./project-locator.js";
-import { buildSkillManifest } from "./skill-registry.js";
-import { setSkillEnabled } from "./skill-state.js";
-import { errorMessage } from "./utils.js";
-import { isManagedSymlink } from "./link-skills.js";
+import { homePath } from "../shared.js";
+import { findProjectDir } from "../project-locator.js";
+import { buildSkillManifest } from "./registry.js";
+import { setSkillEnabled } from "./state.js";
+import { errorMessage } from "../utils.js";
+import { isManagedSymlink } from "../link/skills.js";
+import { logger } from "../logger.js";
 function normalizeSkillRemovalTarget(skillPath) {
     if (!skillPath)
         return skillPath;
@@ -44,9 +45,8 @@ function removeManagedSkillLink(dest, managedRoot) {
         fs.unlinkSync(dest);
     }
     catch (err) {
-        if (err.code !== "ENOENT" && (process.env.PHREN_DEBUG)) {
-            process.stderr.write(`[phren] removeManagedSkillLink: ${errorMessage(err)}\n`);
-        }
+        if (err.code !== "ENOENT")
+            logger.debug("skill-files", `removeManagedSkillLink: ${errorMessage(err)}`);
     }
 }
 function writeSkillArtifacts(destDir, manifest) {

package/mcp/dist/{skill-registry.js → skill/registry.js}

@@ -1,9 +1,9 @@
 import * as fs from "fs";
 import * as path from "path";
-import { getProjectDirs } from "./shared.js";
-import { parseSkillFrontmatter } from "./link-skills.js";
-import { isSkillEnabled } from "./skill-state.js";
-import { safeProjectPath } from "./utils.js";
+import { getProjectDirs } from "../shared.js";
+import { parseSkillFrontmatter } from "../link/skills.js";
+import { isSkillEnabled } from "./state.js";
+import { safeProjectPath } from "../utils.js";
 function normalizeCommand(raw, fallbackName) {
     const value = typeof raw === "string" && raw.trim() ? raw.trim() : `/${fallbackName}`;
     return value.startsWith("/") ? value : `/${value}`;
@@ -223,7 +223,7 @@ export function getAllSkills(phrenPath, profile) {
     }
     return all;
 }
-export function getLocalSkills(phrenPath, scope) {
+function getLocalSkills(phrenPath, scope) {
     if (scope.toLowerCase() === "global")
         return getGlobalSkills(phrenPath);
     return getProjectLocalSkills(phrenPath, scope);

package/mcp/dist/{skill-state.js → skill/state.js}

@@ -1,4 +1,4 @@
-import { readInstallPreferences, writeInstallPreferences } from "./init-preferences.js";
+import { readInstallPreferences, writeInstallPreferences } from "../init/preferences.js";
 function skillStateKey(scope, name) {
     return `${scope}:${name.replace(/\.md$/i, "").trim().toLowerCase()}`;
 }
@@ -23,6 +23,3 @@ export function setSkillEnabled(phrenPath, scope, name, enabled) {
         disabledSkills: Object.keys(disabled).length ? disabled : undefined,
     });
 }
-export function getSkillStateKey(scope, name) {
-    return skillStateKey(scope, name);
-}

package/mcp/dist/startup-embedding.js

@@ -1,10 +1,10 @@
 import { debugLog } from "./shared.js";
-import { decodeStringRow, queryRows } from "./shared-index.js";
+import { decodeStringRow, queryRows } from "./shared/index.js";
 import { errorMessage } from "./utils.js";
 /** Throttle delay between embedding requests in the background embed loop. */
 const BACKGROUND_EMBED_THROTTLE_MS = 50;
 async function loadWarmupDeps() {
-    const { checkOllamaAvailable, embedText, getEmbeddingModel, getOllamaUrl } = await import("./shared-ollama.js");
+    const { checkOllamaAvailable, embedText, getEmbeddingModel, getOllamaUrl } = await import("./shared/ollama.js");
     return {
         checkOllamaAvailable,
         embedText,

package/mcp/dist/status.js

@@ -2,15 +2,16 @@ import * as fs from "fs";
 import * as path from "path";
 import { fileURLToPath } from "url";
 import { findPhrenPath, getProjectDirs, EXEC_TIMEOUT_QUICK_MS, debugLog, isRecord, hookConfigPath, homeDir, readRootManifest, } from "./shared.js";
-import { buildIndex, detectProject, findFtsCacheForPath, listIndexedDocumentPaths, queryRows } from "./shared-index.js";
-import { mergeConfig, getWorkflowPolicy } from "./shared-governance.js";
-import { getMcpEnabledPreference, getHooksEnabledPreference } from "./init.js";
+import { buildIndex, detectProject, findFtsCacheForPath, listIndexedDocumentPaths, queryRows } from "./shared/index.js";
+import { mergeConfig, getWorkflowPolicy } from "./shared/governance.js";
+import { getMcpEnabledPreference, getHooksEnabledPreference } from "./init/init.js";
 import { getTelemetrySummary } from "./telemetry.js";
 import { runGit as runGitShared, errorMessage } from "./utils.js";
-import { readRuntimeHealth, resolveTaskFilePath } from "./data-access.js";
+import { logger } from "./logger.js";
+import { readRuntimeHealth, resolveTaskFilePath } from "./data/access.js";
 import { resolveRuntimeProfile } from "./runtime-profile.js";
 import { renderPhrenArt } from "./phren-art.js";
-import { RESET, BOLD, DIM, GREEN, YELLOW, RED, CYAN } from "./shell-render.js";
+import { RESET, BOLD, DIM, GREEN, YELLOW, RED, CYAN } from "./shell/render.js";
 const __dirname = path.dirname(fileURLToPath(import.meta.url));
 function readPackageVersion() {
     try {
@@ -20,7 +21,7 @@ function readPackageVersion() {
     }
     catch (err) {
         if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] readPackageVersion: ${errorMessage(err)}\n`);
+            logger.debug("status", `readPackageVersion: ${errorMessage(err)}`);
         return "unknown";
     }
 }
@@ -91,7 +92,7 @@ export async function runStatus() {
         }
         catch (err) {
             if ((process.env.PHREN_DEBUG))
-                process.stderr.write(`[phren] statusConfig: ${errorMessage(err)}\n`);
+                logger.debug("status", `statusConfig: ${errorMessage(err)}`);
         }
     }
     // Phren path and config
@@ -125,7 +126,7 @@ export async function runStatus() {
             }
             catch (err) {
                 if ((process.env.PHREN_DEBUG))
-                    process.stderr.write(`[phren] statusWorkspaceMcp parse: ${errorMessage(err)}\n`);
+                    logger.debug("status", `statusWorkspaceMcp parse: ${errorMessage(err)}`);
             }
         }
     }
@@ -143,7 +144,7 @@ export async function runStatus() {
             }
             catch (err) {
                 if ((process.env.PHREN_DEBUG))
-                    process.stderr.write(`[phren] statusHooks settingsParse: ${errorMessage(err)}\n`);
+                    logger.debug("status", `statusHooks settingsParse: ${errorMessage(err)}`);
             }
         }
     }
@@ -174,15 +175,15 @@ export async function runStatus() {
     }
     catch (err) {
         if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] statusFtsIndex: ${errorMessage(err)}\n`);
+            logger.debug("status", `statusFtsIndex: ${errorMessage(err)}`);
     }
     const ftsLabel = ftsIndexOk
         ? `${GREEN}ok${RESET} ${DIM}(${ftsIndexSize > 0 ? `${(ftsIndexSize / 1024).toFixed(0)} KB` : `${ftsDocCount ?? 0} docs`})${RESET}`
         : `${YELLOW}not built${RESET} ${DIM}(run a search to build)${RESET}`;
     console.log(`  ${DIM}fts${RESET}      ${ftsLabel}`);
     try {
-        const { getOllamaUrl, checkOllamaAvailable, checkModelAvailable, getEmbeddingModel } = await import("./shared-ollama.js");
-        const { getEmbeddingCache, formatEmbeddingCoverage } = await import("./shared-embedding-cache.js");
+        const { getOllamaUrl, checkOllamaAvailable, checkModelAvailable, getEmbeddingModel } = await import("./shared/ollama.js");
+        const { getEmbeddingCache, formatEmbeddingCoverage } = await import("./shared/embedding-cache.js");
         const ollamaUrl = getOllamaUrl();
         if (!ollamaUrl) {
             console.log(`  ${DIM}semantic${RESET} ${DIM}disabled (optional)${RESET}`);
@@ -209,7 +210,7 @@ export async function runStatus() {
     }
     catch (err) {
         if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] statusSemantic: ${errorMessage(err)}\n`);
+            logger.debug("status", `statusSemantic: ${errorMessage(err)}`);
     }
     // Agent integration status
     function hasPhrenEntry(filePath) {
@@ -221,7 +222,7 @@ export async function runStatus() {
         }
         catch (err) {
             if ((process.env.PHREN_DEBUG))
-                process.stderr.write(`[phren] hasPhrenEntry: ${errorMessage(err)}\n`);
+                logger.debug("status", `hasPhrenEntry: ${errorMessage(err)}`);
             return false;
         }
     }

package/mcp/dist/{tasks-github.js → task/github.js}

@@ -1,8 +1,8 @@
 import * as fs from "fs";
 import * as path from "path";
 import { execFileSync } from "child_process";
-import { EXEC_TIMEOUT_MS, phrenErr, phrenOk, PhrenError } from "./shared.js";
-import { errorMessage, resolveExecCommand } from "./utils.js";
+import { EXEC_TIMEOUT_MS, phrenErr, phrenOk, PhrenError } from "../shared.js";
+import { errorMessage, resolveExecCommand } from "../utils.js";
 const GITHUB_REPO_URL = /https:\/\/github\.com\/([A-Za-z0-9_.-]+\/[A-Za-z0-9_.-]+)(?:\/|\b|$)/;
 const GITHUB_ISSUE_URL = /https:\/\/github\.com\/([A-Za-z0-9_.-]+\/[A-Za-z0-9_.-]+)\/issues\/(\d+)(?:[?#][^\s]*)?$/;
 export function parseGithubIssueUrl(url) {
@@ -16,6 +16,7 @@ export function parseGithubIssueUrl(url) {
         url: match[0],
     };
 }
+/** @internal Exported for tests. */
 export function extractGithubRepoFromText(content) {
     const match = content.match(GITHUB_REPO_URL);
     return match?.[1];

package/mcp/dist/{task-hygiene.js → task/hygiene.js}

@@ -1,7 +1,8 @@
 import * as fs from "fs";
 import * as path from "path";
-import { isTaskFileName, readTasks } from "./data-tasks.js";
-import { STOP_WORDS, extractKeywords, errorMessage } from "./utils.js";
+import { isTaskFileName, readTasks } from "../data/tasks.js";
+import { STOP_WORDS, extractKeywords, errorMessage } from "../utils.js";
+import { logger } from "../logger.js";
 const TEXT_EXTENSIONS = new Set([
     ".cjs",
     ".css",
@@ -141,8 +142,7 @@ function collectCorpus(root) {
                 texts.push(fs.readFileSync(fullPath, "utf8").slice(0, MAX_TEXT_BYTES).toLowerCase());
             }
             catch (err) {
-                if ((process.env.PHREN_DEBUG))
-                    process.stderr.write(`[phren] task hygiene read ${fullPath}: ${errorMessage(err)}\n`);
+                logger.debug("task-hygiene", `task hygiene read ${fullPath}: ${errorMessage(err)}`);
             }
             if (filesSeen >= MAX_FILES_PER_ROOT)
                 break;

package/mcp/dist/{task-lifecycle.js → task/lifecycle.js}

@@ -1,11 +1,11 @@
 import * as fs from "fs";
-import { addTask, completeTask, readTasks, resolveTaskItem, updateTask, } from "./data-access.js";
-import { parseGithubIssueUrl, resolveProjectGithubRepo } from "./tasks-github.js";
-import { getProactivityLevelForTask, shouldAutoCaptureTaskForLevel, hasExecutionIntent, hasDiscoveryIntent, hasSuppressTaskIntent, hasCodeChangeContext } from "./proactivity.js";
-import { getWorkflowPolicy } from "./shared-governance.js";
-import { debugLog, sessionMarker } from "./shared.js";
-import { errorMessage } from "./utils.js";
-import { incrementSessionTasksCompleted } from "./mcp-session.js";
+import { addTask, completeTask, readTasks, resolveTaskItem, updateTask, } from "../data/access.js";
+import { parseGithubIssueUrl, resolveProjectGithubRepo } from "./github.js";
+import { getProactivityLevelForTask, shouldAutoCaptureTaskForLevel, hasExecutionIntent, hasDiscoveryIntent, hasSuppressTaskIntent, hasCodeChangeContext } from "../proactivity.js";
+import { getWorkflowPolicy } from "../shared/governance.js";
+import { debugLog, sessionMarker } from "../shared.js";
+import { errorMessage } from "../utils.js";
+import { incrementSessionTasksCompleted } from "../tools/session.js";
 const ACTION_PREFIX_RE = /^(?:please\s+|can you\s+|could you\s+|would you\s+|i want you to\s+|i want to\s+|let(?:'|’)s\s+|lets\s+|help me\s+)/i;
 const EXPLICIT_TASK_PREFIX_RE = /^(?:add(?:\s+(?:this|that|it))?\s+(?:to\s+(?:the\s+)?)?(?:task|todo(?:\s+list)?|task(?:\s+list)?)|add\s+(?:a\s+)?task|put(?:\s+(?:this|that|it))?\s+(?:in|on)\s+(?:the\s+)?(?:task|todo(?:\s+list)?|task(?:\s+list)?))\s*(?::|-|,)?\s*/i;
 const NON_ACTIONABLE_RE = /\b(brainstorm|idea|ideas|maybe|what if|should we|could we|would it make sense|question|explain|why is|how does)\b/i;
@@ -80,7 +80,7 @@ function clearTaskSessionState(phrenPath, sessionId) {
         debugLog(`task lifecycle clear session ${sessionId}: ${errorMessage(err)}`);
     }
 }
-export function getTaskMode(phrenPath) {
+function getTaskMode(phrenPath) {
     return getWorkflowPolicy(phrenPath).taskMode;
 }
 function isActionablePrompt(prompt, intent) {
@@ -330,11 +330,6 @@ export function finalizeTaskSession(args) {
         return;
     }
 }
-export function clearTaskSession(phrenPath, sessionId) {
-    if (!sessionId)
-        return;
-    clearTaskSessionState(phrenPath, sessionId);
-}
 /**
  * Return the active TaskItem tracked for a session+project, if any.
  * Used by mcp-finding.ts to link findings to active tasks.

package/mcp/dist/telemetry.js

@@ -2,6 +2,7 @@ import * as fs from "fs";
 import * as path from "path";
 import { runtimeDir } from "./shared.js";
 import { errorMessage } from "./utils.js";
+import { logger } from "./logger.js";
 // In-memory buffers keyed by phrenPath to batch disk writes
 // Keeping per-path buffers avoids silently losing events when the active path changes.
 const buffers = new Map();
@@ -26,8 +27,7 @@ function loadFromDisk(phrenPath) {
         };
     }
     catch (err) {
-        if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] telemetry loadFromDisk: ${errorMessage(err)}\n`);
+        logger.debug("telemetry loadFromDisk", errorMessage(err));
         return defaults;
     }
 }
@@ -58,8 +58,7 @@ function flushTelemetryForPath(phrenPath) {
         fs.writeFileSync(file, JSON.stringify(data, null, 2) + "\n");
     }
     catch (err) {
-        if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] telemetry flush: ${errorMessage(err)}\n`);
+        logger.debug("telemetry flush", errorMessage(err));
     }
     pendingCounts.set(phrenPath, 0);
 }

package/mcp/dist/tool-registry.js

@@ -2,18 +2,18 @@ import * as fs from "fs";
 import * as path from "path";
 import { fileURLToPath } from "url";
 const CATEGORY_BY_MODULE = {
-    "mcp-search": "Search and browse",
-    "mcp-tasks": "Task management",
-    "mcp-finding": "Finding capture",
-    "mcp-memory": "Memory quality",
-    "mcp-data": "Data management",
-    "mcp-graph": "Fragments and graph",
-    "mcp-session": "Session management",
-    "mcp-ops": "Operations and review",
-    "mcp-skills": "Skills management",
-    "mcp-hooks": "Hooks management",
-    "mcp-config": "Configuration",
-    "mcp-extract": "Extraction",
+    "search": "Search and browse",
+    "tasks": "Task management",
+    "finding": "Finding capture",
+    "memory": "Memory quality",
+    "data": "Data management",
+    "graph": "Fragments and graph",
+    "session": "Session management",
+    "ops": "Operations and review",
+    "skills": "Skills management",
+    "hooks": "Hooks management",
+    "config": "Configuration",
+    "extract": "Extraction",
 };
 const MODULE_ORDER = Object.keys(CATEGORY_BY_MODULE);
 const __dirname = path.dirname(fileURLToPath(import.meta.url));
@@ -45,7 +45,7 @@ function parseModuleTools(moduleName, source) {
         });
     }
     // Handle loop-registered tools: { tool: "name", ... } patterns followed by registerTool(action.tool, ...)
-    const loopPattern = /for\s*\(const\s+(\w+)\s+of\s+\[([\s\S]*?)\]\s*(?:as\s+const\s*)?\)\s*\{\s*server\.registerTool\(\s*\1\.tool\s*,\s*\{([\s\S]*?)\}\s*,/g;
+    const loopPattern = /for\s*\(const\s+(\w+)\s+of\s+\[([\s\S]*?)\]\s*(?:as\s+const\s*)?\)\s*\{[\s\S]*?server\.registerTool\(\s*\1\.tool\s*,\s*\{([\s\S]*?)\}\s*,/g;
     for (const loopMatch of source.matchAll(loopPattern)) {
         const [, , itemsBlock, configBlock] = loopMatch;
         const itemPattern = /\{\s*tool:\s*"([^"]+)"[^}]*verb:\s*"([^"]+)"/g;
@@ -66,11 +66,23 @@ function parseModuleTools(moduleName, source) {
 export function getRegisteredTools() {
     const dir = sourceDir();
     const entries = [];
+    const toolsDir = path.join(dir, "tools");
     for (const moduleName of MODULE_ORDER) {
-        const tsPath = path.join(dir, `${moduleName}.ts`);
-        const jsPath = path.join(dir, `${moduleName}.js`);
-        const sourcePath = fs.existsSync(tsPath) ? tsPath : jsPath;
-        if (!fs.existsSync(sourcePath))
+        // Tool files may live in the tools/ subdirectory or alongside tool-registry.ts
+        let sourcePath;
+        for (const base of [toolsDir, dir]) {
+            const tsPath = path.join(base, `${moduleName}.ts`);
+            const jsPath = path.join(base, `${moduleName}.js`);
+            if (fs.existsSync(tsPath)) {
+                sourcePath = tsPath;
+                break;
+            }
+            if (fs.existsSync(jsPath)) {
+                sourcePath = jsPath;
+                break;
+            }
+        }
+        if (!sourcePath)
             continue;
         entries.push(...parseModuleTools(moduleName, fs.readFileSync(sourcePath, "utf8")));
     }