@phren/cli 0.0.32 → 0.0.34

package/mcp/dist/init-uninstall.js

@@ -428,6 +428,28 @@ 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-walkthrough.js

@@ -300,31 +300,26 @@ export 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");
             }
         }
     }

package/mcp/dist/link/doctor.js

@@ -402,6 +402,15 @@ export async function runDoctor(phrenPath, fix = false, checkData = false) {
                 : `${tool} wrapper missing or not first in PATH`,
         });
     }
+    // Check phren CLI wrapper
+    const phrenCliActive = isWrapperActive("phren");
+    checks.push({
+        name: "wrapper:phren-cli",
+        ok: phrenCliActive,
+        detail: phrenCliActive
+            ? "phren CLI wrapper active via ~/.local/bin/phren"
+            : "phren CLI wrapper missing — run init to install, or npm i -g @phren/cli",
+    });
     if (fix) {
         const repaired = repairPreexistingInstall(phrenPath);
         const details = [];

package/mcp/dist/package-metadata.js

@@ -3,7 +3,7 @@ import * as path from "path";
 import { fileURLToPath } from "url";
 const __dirname = path.dirname(fileURLToPath(import.meta.url));
 export const ROOT = path.join(__dirname, "..", "..");
-export const PACKAGE_JSON_PATH = path.join(ROOT, "package.json");
+const PACKAGE_JSON_PATH = path.join(ROOT, "package.json");
 function readPackageJson() {
     return JSON.parse(fs.readFileSync(PACKAGE_JSON_PATH, "utf8"));
 }

package/mcp/dist/phren-art.js

@@ -1,20 +1,9 @@
 /**
- * Phren character ASCII/Unicode art, animation engine, and spinner for CLI presence.
+ * Phren character ASCII/Unicode art for CLI presence.
  *
  * Based on the pixel art: purple 8-bit brain with diamond eyes,
  * smile, little legs, and cyan sparkle.
- *
- * Animation system provides lifelike movement through composable effects:
- * bob, blink, sparkle, and lean — all driven by setTimeout with randomized
- * intervals for organic timing.
  */
-const ESC = "\x1b[";
-const RESET = `${ESC}0m`;
-const PURPLE = `${ESC}35m`; // magenta — body
-const BRIGHT_PURPLE = `${ESC}95m`; // bright magenta — highlights
-const CYAN = `${ESC}96m`; // bright cyan — sparkle
-const DARK_PURPLE = `${ESC}38;5;57m`; // deep purple — shadow/outline
-// ── Art constants (24px wide, truecolor half-blocks) ─────────────────────────
 /**
  * Phren truecolor art (24px wide, generated from phren-transparent.png).
  * Uses half-block ▀ with RGB foreground+background for pixel-faithful rendering.
@@ -35,32 +24,18 @@ export const PHREN_ART = [
     "                        ",
 ];
 // ── Sparkle row: the cyan pixels at row 2 ────────────────────────────────────
-// Sparkle uses ▄ half-blocks with cyan truecolor. For animation we cycle through
-// decorative unicode characters at different brightness levels.
 const SPARKLE_ROW = 2;
-const SPARKLE_CHARS = ["\u2726", "\u2727", "\u2736", " "]; // ✦ ✧ ✶ (dim/blank)
-// ── Eye detection: dark navy pixels in row 6 (fg R<30, G<45, B<120) ──────────
-// Row 6 has two eye pixels at segments 1 and 5 (visual positions 7 and 11).
-// When blinking, we replace their dark fg color with the surrounding body purple.
+const SPARKLE_CHARS = ["\u2726", "\u2727", "\u2736", " "];
+// ── Eye detection: dark navy pixels in row 6 ─────────────────────────────────
 const EYE_ROW = 6;
-// Dark-pixel fg threshold
 const EYE_R_MAX = 30;
 const EYE_G_MAX = 45;
 const EYE_B_MAX = 120;
-// Body-purple color to use when "closing" eyes (average of surrounding pixels)
 const BLINK_COLOR = "146;130;250";
-/**
- * Flip a single art line horizontally. Reverses the order of colored pixel
- * segments and swaps leading/trailing whitespace so the character faces right.
- * Half-block characters (▀ ▄) are horizontally symmetric so no char swap needed.
- */
 function flipLine(line) {
     const stripped = line.replace(/\x1b\[[^m]*m/g, "");
     const leadSpaces = stripped.match(/^( *)/)[1].length;
     const trailSpaces = stripped.match(/( *)$/)[1].length;
-    // Parse pixel segments: each is one or two ANSI color codes followed by a block char.
-    // We strip any leading reset (\x1b[0m) from captured codes — it's an artifact from
-    // the original per-pixel reset pattern and will be re-added during reassembly.
     const pixels = [];
     const pixelRegex = /((?:\x1b\[[^m]*m)+)([\u2580\u2584])/g;
     let match;
@@ -70,7 +45,7 @@ function flipLine(line) {
             pixels.push({ codes, char: match[2] });
     }
     if (pixels.length === 0)
-        return line; // blank or space-only line
+        return line;
     const reversed = [...pixels].reverse();
     const newLead = " ".repeat(trailSpaces);
     const newTrail = " ".repeat(leadSpaces);
@@ -81,26 +56,14 @@ function flipLine(line) {
     result += newTrail;
     return result;
 }
-/**
- * Generate horizontally flipped art (facing right).
- */
 function generateFlippedArt(art) {
     return art.map(flipLine);
 }
-/** Pre-computed right-facing art */
 export const PHREN_ART_RIGHT = generateFlippedArt(PHREN_ART);
-/** Random integer in [min, max] inclusive */
 function randInt(min, max) {
     return Math.floor(Math.random() * (max - min + 1)) + min;
 }
-/**
- * Replace eye pixels on a single line with the blink color.
- * Eye pixels are identified by their dark navy fg color (R<30, G<45, B<120).
- * We replace the fg color code while preserving the bg code and character.
- */
 function applyBlinkToLine(line) {
-    // Match ANSI color sequences: each pixel is \e[38;2;R;G;Bm (optionally with \e[48;2;...m) then a block char
-    // We scan for fg codes that match the eye threshold and replace them with the blink color
     return line.replace(/\x1b\[38;2;(\d+);(\d+);(\d+)m/g, (full, rStr, gStr, bStr) => {
         const r = Number(rStr);
         const g = Number(gStr);
@@ -111,44 +74,24 @@ function applyBlinkToLine(line) {
         return full;
     });
 }
-/**
- * Replace the sparkle pixels on the sparkle row with the current sparkle character.
- * The sparkle row has two cyan ▄ half-blocks. During sparkle animation we replace
- * them with decorative Unicode characters from SPARKLE_CHARS.
- */
 function applySparkleToLine(line, frame, active) {
     if (!active)
         return line;
     const sparkleChar = SPARKLE_CHARS[frame % SPARKLE_CHARS.length];
     if (sparkleChar === " ") {
-        // Dim: replace the cyan-colored segments with spaces (they disappear)
         return line.replace(/\x1b\[38;2;\d+;2\d\d;2\d\dm[\u2580\u2584]\x1b\[0m/g, " ");
     }
-    // Replace the half-block characters with the sparkle unicode char, keeping the cyan color
     return line.replace(/(\x1b\[38;2;\d+;2\d\d;2\d\dm)[\u2580\u2584](\x1b\[0m)/g, `$1${sparkleChar}$2`);
 }
-/**
- * Apply lean (horizontal shift) to a line.
- * Positive offset = shift right (prepend spaces, trim from end).
- * Negative offset = shift left (trim from start, append spaces).
- */
 function applyLean(line, offset) {
     if (offset === 0)
         return line;
     if (offset > 0) {
-        // Shift right: prepend spaces
         return " ".repeat(offset) + line;
     }
-    // Shift left: remove leading spaces (up to |offset|)
     const trimCount = Math.min(-offset, line.match(/^( *)/)[1].length);
     return line.slice(trimCount);
 }
-/**
- * Create an animated phren character controller.
- *
- * @param options.facing - 'left' (default, original) or 'right' (flipped)
- * @param options.size - art width; unused but reserved for future scaling (default 24)
- */
 export function createPhrenAnimator(options) {
     const facing = options?.facing ?? "left";
     const baseArt = facing === "right" ? PHREN_ART_RIGHT : PHREN_ART;
@@ -164,22 +107,18 @@ export function createPhrenAnimator(options) {
         const t = setTimeout(fn, ms);
         timers.push(t);
     }
-    // ── Bob animation: toggles bobUp every ~500ms ──────────────────────────
     function scheduleBob() {
         scheduleTimer(() => {
             state.bobUp = !state.bobUp;
             scheduleBob();
         }, 500);
     }
-    // ── Blink animation: eyes close for 150ms, random 2-8s intervals ──────
     function scheduleBlink() {
         const interval = randInt(2000, 8000);
         scheduleTimer(() => {
-            // Perform blink
             state.isBlinking = true;
             scheduleTimer(() => {
                 state.isBlinking = false;
-                // 30% chance of double-blink
                 if (Math.random() < 0.3) {
                     scheduleTimer(() => {
                         state.isBlinking = true;
@@ -195,9 +134,7 @@ export function createPhrenAnimator(options) {
             }, 150);
         }, interval);
     }
-    // ── Sparkle animation: fast cycle during bursts, long pauses between ───
     function scheduleSparkle() {
-        // Wait 1-5 seconds before next sparkle burst
         const pause = randInt(1000, 5000);
         scheduleTimer(() => {
             state.sparkleActive = true;
@@ -207,7 +144,6 @@ export function createPhrenAnimator(options) {
     }
     function sparkleStep(step) {
         if (step >= SPARKLE_CHARS.length) {
-            // Burst complete
             state.sparkleActive = false;
             scheduleSparkle();
             return;
@@ -217,7 +153,6 @@ export function createPhrenAnimator(options) {
             sparkleStep(step + 1);
         }, 200);
     }
-    // ── Lean animation: shift 1 col left or right every 4-10s, hold 1-2s ──
     function scheduleLean() {
         const interval = randInt(4000, 10000);
         scheduleTimer(() => {
@@ -234,19 +169,15 @@ export function createPhrenAnimator(options) {
         getFrame() {
             let lines = baseArt.map((line, i) => {
                 let result = line;
-                // Apply blink to the eye row
                 if (state.isBlinking && i === EYE_ROW) {
                     result = applyBlinkToLine(result);
                 }
-                // Apply sparkle to sparkle row
                 if (i === SPARKLE_ROW) {
                     result = applySparkleToLine(result, state.sparkleFrame, state.sparkleActive);
                 }
-                // Apply lean
                 result = applyLean(result, state.leanOffset);
                 return result;
             });
-            // Apply bob: when bobUp, prepend a blank line (shift everything down visually)
             if (state.bobUp) {
                 lines = ["", ...lines.slice(0, -1)];
             }
@@ -266,56 +197,9 @@ export function createPhrenAnimator(options) {
         },
     };
 }
-// ── Startup frames (pre-baked, no timers) ────────────────────────────────────
-/**
- * Returns 4 pre-baked animation frames for shell startup display.
- * No timers needed — the caller cycles through them manually.
- *
- * Frames: [neutral, bob-up, neutral, bob-down(sparkle)]
- *
- * @param facing - 'left' (default) or 'right'
- */
-export function getPhrenStartupFrames(facing) {
-    const art = facing === "right" ? PHREN_ART_RIGHT : PHREN_ART;
-    // Frame 0: neutral
-    const frame0 = [...art];
-    // Frame 1: bob up (prepend blank line, drop last line)
-    const frame1 = ["", ...art.slice(0, -1)];
-    // Frame 2: neutral (same as frame 0)
-    const frame2 = [...art];
-    // Frame 3: bob down with sparkle burst — shift down by removing first line, append blank
-    const frame3WithSparkle = art.map((line, i) => {
-        if (i === SPARKLE_ROW) {
-            return applySparkleToLine(line, 0, true); // ✦ sparkle
-        }
-        return line;
-    });
-    const frame3 = [...frame3WithSparkle.slice(1), ""];
-    return [frame0, frame1, frame2, frame3];
-}
-// ── Legacy exports (unchanged) ───────────────────────────────────────────────
-/** Single-line compact phren for inline use */
-export const PHREN_INLINE = `${PURPLE}◆${RESET}`;
-/** Phren spinner frames for search/sync operations — cycles through in purple */
-export const PHREN_SPINNER_FRAMES = [
-    `${BRIGHT_PURPLE}◆${RESET}`,
-    `${PURPLE}◇${RESET}`,
-    `${CYAN}✦${RESET}`,
-    `${PURPLE}✧${RESET}`,
-    `${BRIGHT_PURPLE}◆${RESET}`,
-    `${DARK_PURPLE}◇${RESET}`,
-];
-/** Default spinner interval in ms */
-export const PHREN_SPINNER_INTERVAL_MS = 120;
 /**
  * Return the phren art as a single string, optionally indented.
  */
 export function renderPhrenArt(indent = "") {
     return PHREN_ART.map(line => indent + line).join("\n");
 }
-/**
- * Get a spinner frame by index (wraps around automatically).
- */
-export function spinnerFrame(tick) {
-    return PHREN_SPINNER_FRAMES[tick % PHREN_SPINNER_FRAMES.length];
-}

package/mcp/dist/proactivity.js

@@ -21,7 +21,7 @@ function resolveProactivityPhrenPath(explicitPhrenPath) {
     return explicitPhrenPath ?? findPhrenPath();
 }
 /** Read per-user preferences from ~/.phren/.users/<actor>/preferences.json. Actor from PHREN_ACTOR env var. */
-export function readUserPreferences(explicitPhrenPath) {
+function readUserPreferences(explicitPhrenPath) {
     const phrenPath = resolveProactivityPhrenPath(explicitPhrenPath);
     if (!phrenPath)
         return {};

package/mcp/dist/project-topics.js

@@ -4,6 +4,7 @@ import * as path from "path";
 import { debugLog } from "./shared.js";
 import { withFileLock } from "./shared/governance.js";
 import { STOP_WORDS, errorMessage, extractKeywords, isValidProjectName, safeProjectPath } from "./utils.js";
+import { walkDirectory } from "./shared/data-utils.js";
 const TOPIC_CONFIG_FILENAME = "topic-config.json";
 const AUTO_TOPIC_MARKER_RE = /^<!--\s*phren:auto-topic(?:\s+slug=([a-z0-9_-]+))?\s*-->$/;
 const ARCHIVED_SECTION_RE = /^## Archived (\d{4}-\d{2}-\d{2})$/;
@@ -303,7 +304,7 @@ function normalizeKeyword(raw) {
         .replace(/\s+/g, " ")
         .trim();
 }
-export function normalizeTopicSlug(raw) {
+function normalizeTopicSlug(raw) {
     return raw
         .trim()
         .toLowerCase()
@@ -384,10 +385,7 @@ function topicConfigPath(phrenPath, project) {
 function projectDirPath(phrenPath, project) {
     return safeProjectPath(phrenPath, project);
 }
-export function topicReferenceDir(phrenPath, project) {
-    return safeProjectPath(phrenPath, project, "reference", "topics");
-}
-export function topicReferenceRelativePath(slug) {
+function topicReferenceRelativePath(slug) {
     return path.posix.join("reference", "topics", `${slug}.md`);
 }
 export function topicReferencePath(phrenPath, project, slug) {
@@ -575,7 +573,7 @@ export function readProjectTopics(phrenPath, project) {
     }
     return { source: "custom", topics: normalized, domain: typeof parsed.domain === "string" ? parsed.domain : undefined };
 }
-export function readPinnedTopics(phrenPath, project) {
+function readPinnedTopics(phrenPath, project) {
     const configPath = topicConfigPath(phrenPath, project);
     if (!configPath || !fs.existsSync(configPath))
         return [];
@@ -675,27 +673,14 @@ function normalizeBullet(line) {
 }
 function collectArchivedBulletsRecursively(dirPath) {
     const bullets = new Set();
-    if (!fs.existsSync(dirPath))
-        return bullets;
-    const stack = [dirPath];
-    while (stack.length > 0) {
-        const current = stack.pop();
-        for (const entry of fs.readdirSync(current, { withFileTypes: true })) {
-            const fullPath = path.join(current, entry.name);
-            if (entry.isDirectory()) {
-                stack.push(fullPath);
-                continue;
-            }
-            if (!entry.isFile() || !entry.name.endsWith(".md"))
+    for (const filePath of walkDirectory(dirPath)) {
+        const content = fs.readFileSync(filePath, "utf8");
+        for (const line of content.split("\n")) {
+            if (!line.startsWith("- "))
                 continue;
-            const content = fs.readFileSync(fullPath, "utf8");
-            for (const line of content.split("\n")) {
-                if (!line.startsWith("- "))
-                    continue;
-                const normalized = normalizeBullet(line);
-                if (normalized)
-                    bullets.add(normalized);
-            }
+            const normalized = normalizeBullet(line);
+            if (normalized)
+                bullets.add(normalized);
         }
     }
     return bullets;
@@ -797,23 +782,7 @@ function parseLegacyTopicEntries(content, project) {
     return { slug: fallbackSlug, entries };
 }
 function readReferenceMarkdownFiles(referenceDir) {
-    if (!fs.existsSync(referenceDir))
-        return [];
-    const files = [];
-    const stack = [referenceDir];
-    while (stack.length > 0) {
-        const current = stack.pop();
-        for (const entry of fs.readdirSync(current, { withFileTypes: true })) {
-            const fullPath = path.join(current, entry.name);
-            if (entry.isDirectory()) {
-                stack.push(fullPath);
-                continue;
-            }
-            if (entry.isFile() && entry.name.endsWith(".md"))
-                files.push(fullPath);
-        }
-    }
-    return files.sort();
+    return walkDirectory(referenceDir).sort();
 }
 function relativeToProject(projectDir, filePath) {
     return path.relative(projectDir, filePath).replace(/\\/g, "/");
@@ -835,7 +804,7 @@ function safeStatIso(filePath) {
         return "";
     }
 }
-export function listProjectTopicDocs(phrenPath, project, topics) {
+function listProjectTopicDocs(phrenPath, project, topics) {
     const projectDir = projectDirPath(phrenPath, project);
     if (!projectDir)
         return [];
@@ -885,7 +854,7 @@ export function listProjectReferenceDocs(phrenPath, project, topics) {
     }
     return { topicDocs, otherDocs };
 }
-export function listLegacyTopicDocs(phrenPath, project) {
+function listLegacyTopicDocs(phrenPath, project) {
     const projectDir = projectDirPath(phrenPath, project);
     const referenceDir = safeProjectPath(phrenPath, project, "reference");
     if (!projectDir || !referenceDir || !fs.existsSync(referenceDir))
@@ -1042,6 +1011,7 @@ export function suggestTopics(phrenPath, project, topics) {
     }
     return deduped;
 }
+/** @internal Exported for tests. */
 export const suggestProjectTopics = suggestTopics;
 export function getProjectTopicsResponse(phrenPath, project) {
     const { source, topics } = readProjectTopics(phrenPath, project);
@@ -1054,7 +1024,7 @@ export function getProjectTopicsResponse(phrenPath, project) {
         topicDocs: listProjectTopicDocs(phrenPath, project, topics),
     };
 }
-export function resolveReferenceContentPath(phrenPath, project, file) {
+function resolveReferenceContentPath(phrenPath, project, file) {
     if (!isValidProjectName(project) || !file || file.includes("\0"))
         return null;
     if (!file.endsWith(".md"))

package/mcp/dist/provider-adapters.js

@@ -35,7 +35,7 @@ function normalizeWindowsPathToWsl(input) {
 function uniqStrings(values) {
     return Array.from(new Set(values.filter((value) => Boolean(value && value.trim()))));
 }
-export function pickExistingFile(candidates) {
+function pickExistingFile(candidates) {
     for (const candidate of candidates) {
         if (fs.existsSync(candidate))
             return candidate;

package/mcp/dist/runtime-profile.js

@@ -1,5 +1,5 @@
 import { resolveActiveProfile } from "./profile-store.js";
-export function requestedProfileFromEnv() {
+function requestedProfileFromEnv() {
     const profile = (process.env.PHREN_PROFILE)?.trim();
     return profile ? profile : undefined;
 }

package/mcp/dist/shared/data-utils.js

@@ -15,6 +15,31 @@ export function withSafeLock(filePath, fn) {
         throw err;
     }
 }
+/**
+ * Recursively walk a directory and return paths of files matching an optional filter.
+ * Defaults to `.md` files only. Uses an iterative stack to avoid recursion limits.
+ */
+export function walkDirectory(root, filter) {
+    const accept = filter ?? ((name) => name.endsWith(".md"));
+    const results = [];
+    if (!fs.existsSync(root))
+        return results;
+    const stack = [root];
+    while (stack.length > 0) {
+        const current = stack.pop();
+        for (const entry of fs.readdirSync(current, { withFileTypes: true })) {
+            const fullPath = path.join(current, entry.name);
+            if (entry.isDirectory()) {
+                stack.push(fullPath);
+                continue;
+            }
+            if (entry.isFile() && accept(entry.name)) {
+                results.push(fullPath);
+            }
+        }
+    }
+    return results;
+}
 export function ensureProject(phrenPath, project) {
     if (!isValidProjectName(project))
         return phrenErr(`Project name "${project}" is not valid. Use lowercase letters, numbers, and hyphens (e.g. "my-project").`, PhrenError.INVALID_PROJECT_NAME);

package/mcp/dist/shared/fragment-graph.js

@@ -4,8 +4,10 @@ import { runtimeFile } from "../shared.js";
 import { logger } from "../logger.js";
 import { UNIVERSAL_TECH_TERMS_RE } from "../phren-core.js";
 import { errorMessage } from "../utils.js";
+/** @internal Exported for tests. */
 export function escapeRegex(s) { return s.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); }
-/** Escape SQL LIKE wildcard characters so user input is treated literally. */
+/** Escape SQL LIKE wildcard characters so user input is treated literally.
+ * @internal Exported for tests. */
 export function escapeLike(s) { return s.replace(/[%_\\]/g, '\\$&'); }
 /**
  * Log fragment resolution misses to .runtime/fragment-misses.jsonl.
@@ -41,8 +43,6 @@ export function logFragmentMiss(phrenPath, name, context, project) {
         // Best-effort logging; don't let miss tracking break the caller.
     }
 }
-/** @deprecated Use logFragmentMiss instead */
-export const logEntityMiss = logFragmentMiss;
 // Use the shared universal starter set. Framework/tool specifics are learned
 // dynamically per project via extractDynamicFragments() in content-dedup.ts.
 const PROSE_FRAGMENT_PATTERN = UNIVERSAL_TECH_TERMS_RE;
@@ -110,8 +110,6 @@ export function extractFragmentNames(content) {
     }
     return [...found];
 }
-/** @deprecated Use extractFragmentNames instead */
-export const extractEntityNames = extractFragmentNames;
 function getOrCreateFragment(db, name, type) {
     try {
         db.run("INSERT OR IGNORE INTO entities (name, type, first_seen_at) VALUES (?, ?, ?)", [name, type, new Date().toISOString().slice(0, 10)]);
@@ -190,8 +188,6 @@ export function beginUserFragmentBuildCache(phrenPath, projects) {
         }
     }
 }
-/** @deprecated Use beginUserFragmentBuildCache instead */
-export const beginUserEntityBuildCache = beginUserFragmentBuildCache;
 /** End a build-scoped cache created by beginUserFragmentBuildCache(). */
 export function endUserFragmentBuildCache(phrenPath) {
     const prefix = `${phrenPath}/`;
@@ -202,8 +198,6 @@ export function endUserFragmentBuildCache(phrenPath) {
     if (_activeBuildCacheKeyPrefix === prefix)
         _activeBuildCacheKeyPrefix = null;
 }
-/** @deprecated Use endUserFragmentBuildCache instead */
-export const endUserEntityBuildCache = endUserFragmentBuildCache;
 function parseUserDefinedFragments(phrenPath, project) {
     const claudeMdPath = `${phrenPath}/${project}/CLAUDE.md`;
     const cacheKey = `${phrenPath}/${project}`;
@@ -238,13 +232,11 @@ function parseUserDefinedFragments(phrenPath, project) {
     }
 }
 /** Clear the user fragment cache (call between index builds). */
-export function clearUserFragmentCache() {
+function clearUserFragmentCache() {
     _userFragmentCache.clear();
     _buildUserFragmentCache.clear();
     _activeBuildCacheKeyPrefix = null;
 }
-/** @deprecated Use clearUserFragmentCache instead */
-export const clearUserEntityCache = clearUserFragmentCache;
 // Words that commonly start sentences or appear in titles — not fragment names
 const SENTENCE_START_WORDS = new Set([
     "the", "this", "that", "these", "those", "when", "where", "which", "while",
@@ -362,8 +354,6 @@ export function extractAndLinkFragments(db, content, sourceDoc, phrenPath) {
         }
     }
 }
-/** @deprecated Use extractAndLinkFragments instead */
-export const extractAndLinkEntities = extractAndLinkFragments;
 /**
  * Query related fragments for a given name.
  */
@@ -389,8 +379,6 @@ export function queryFragmentLinks(db, name) {
     }
     return { related };
 }
-/** @deprecated Use queryFragmentLinks instead */
-export const queryEntityLinks = queryFragmentLinks;
 /**
  * Query cross-project fragment relationships.
  * Returns projects and docs that share fragments with the given query.
@@ -444,5 +432,3 @@ export function getFragmentBoostDocs(db, query) {
         return new Set();
     }
 }
-/** @deprecated Use getFragmentBoostDocs instead */
-export const getEntityBoostDocs = getFragmentBoostDocs;