@cubedot/cli 0.1.1 → 0.1.3

package/dist/cli.js

@@ -3,12 +3,12 @@
 // src/cli.ts
 import { Command } from "commander";
 import { fileURLToPath as fileURLToPath4 } from "url";
-import { dirname as dirname4, join as join9 } from "path";
-import { readFileSync as readFileSync9 } from "fs";
+import { dirname as dirname4, join as join10 } from "path";
+import { readFileSync as readFileSync10 } from "fs";
 
 // src/commands/init.ts
 import pc from "picocolors";
-import { readFileSync as readFileSync3 } from "fs";
+import { readFileSync as readFileSync3, existsSync as existsSync3 } from "fs";
 import { join as join3 } from "path";
 
 // src/mcp.ts
@@ -83,7 +83,10 @@ import {
   copyFileSync,
   existsSync,
   mkdirSync,
+  readdirSync,
   readFileSync,
+  rmdirSync,
+  unlinkSync,
   writeFileSync
 } from "fs";
 import { dirname, join } from "path";
@@ -101,13 +104,15 @@ function writeMcpJson(cwd, mcpUrl, projectId, key) {
     } catch {
     }
   }
+  const mcpEndpoint = new URL(mcpUrl);
+  mcpEndpoint.searchParams.set("project", projectId);
   const config = {
     ...existing,
     mcpServers: {
       ...existing.mcpServers ?? {},
       cubedot: {
         type: "http",
-        url: `${mcpUrl}?project=${encodeURIComponent(projectId)}`,
+        url: mcpEndpoint.toString(),
         headers: { Authorization: `ApiKey ${key}` }
       }
     }
@@ -176,17 +181,18 @@ var GITIGNORE_ENTRIES = [
 function updateGitignore(cwd) {
   const path = join(cwd, ".gitignore");
   let content = existsSync(path) ? readFileSync(path, "utf8") : "";
-  const lines = content.split("\n");
-  let changed = false;
+  const existing = content.split("\n");
+  const added = [];
   for (const entry of GITIGNORE_ENTRIES) {
-    if (!lines.some((l) => l.trim() === entry)) {
+    if (!existing.some((l) => l.trim() === entry)) {
       content = content.endsWith("\n") ? content + entry + "\n" : content + "\n" + entry + "\n";
-      changed = true;
+      added.push(entry);
     }
   }
-  if (changed) {
+  if (added.length > 0) {
     writeFileSync(path, content, "utf8");
   }
+  return added;
 }
 function readHashes(cwd) {
   const path = join(cwd, ".cubedot", "sync", "hashes.json");
@@ -206,8 +212,9 @@ function enableMcpServerInSettings(cwd, serverName = "cubedot") {
   const dir = join(cwd, ".claude");
   if (!existsSync(dir)) mkdirSync(dir, { recursive: true });
   const path = join(dir, "settings.json");
+  const existed = existsSync(path);
   let settings = {};
-  if (existsSync(path)) {
+  if (existed) {
     try {
       settings = JSON.parse(readFileSync(path, "utf8"));
     } catch {
@@ -218,6 +225,7 @@ function enableMcpServerInSettings(cwd, serverName = "cubedot") {
     settings["enabledMcpjsonServers"] = [...cur, serverName];
   }
   writeFileSync(path, JSON.stringify(settings, null, 2) + "\n", "utf8");
+  return { created: !existed };
 }
 function readLinks(cwd) {
   const path = join(cwd, ".cubedot", "links.json");
@@ -228,6 +236,76 @@ function readLinks(cwd) {
     return {};
   }
 }
+var MANIFEST_PATH = ".cubedot/install-manifest.json";
+function readInstallManifest(cwd) {
+  const path = join(cwd, MANIFEST_PATH);
+  if (!existsSync(path)) return null;
+  try {
+    return JSON.parse(readFileSync(path, "utf8"));
+  } catch {
+    return null;
+  }
+}
+function writeInstallManifest(cwd, manifest) {
+  writeFileSync(join(cwd, MANIFEST_PATH), JSON.stringify(manifest, null, 2) + "\n", "utf8");
+}
+function stripGitignoreLines(cwd, lines) {
+  const path = join(cwd, ".gitignore");
+  if (!existsSync(path)) return;
+  const content = readFileSync(path, "utf8");
+  const kept = content.split("\n").filter((l) => !lines.includes(l.trim()));
+  while (kept.length > 0 && !kept[kept.length - 1]?.trim()) kept.pop();
+  if (kept.length === 0) {
+    unlinkSync(path);
+  } else {
+    writeFileSync(path, kept.join("\n") + "\n", "utf8");
+  }
+}
+function removeCubedotFromSettings(cwd) {
+  const path = join(cwd, ".claude", "settings.json");
+  if (!existsSync(path)) return;
+  let settings;
+  try {
+    settings = JSON.parse(readFileSync(path, "utf8"));
+  } catch {
+    return;
+  }
+  if (!Array.isArray(settings["enabledMcpjsonServers"])) return;
+  const filtered = settings["enabledMcpjsonServers"].filter(
+    (s) => s !== "cubedot"
+  );
+  if (filtered.length === 0) {
+    delete settings["enabledMcpjsonServers"];
+  } else {
+    settings["enabledMcpjsonServers"] = filtered;
+  }
+  if (Object.keys(settings).length === 0) {
+    unlinkSync(path);
+  } else {
+    writeFileSync(path, JSON.stringify(settings, null, 2) + "\n", "utf8");
+  }
+}
+function stripCubedotMarkers(filePath) {
+  if (!existsSync(filePath)) return;
+  const content = readFileSync(filePath, "utf8");
+  const stripped = content.replace(
+    /<!-- CUBEDOT:START:(\w+) -->[\s\S]*?<!-- CUBEDOT:END:\1 -->\n?/g,
+    ""
+  );
+  const cleaned = stripped.replace(/\n{3,}/g, "\n\n").trimEnd();
+  writeFileSync(filePath, cleaned ? cleaned + "\n" : "", "utf8");
+}
+function tryRmdir(dirPath) {
+  if (!existsSync(dirPath)) return false;
+  try {
+    const entries = readdirSync(dirPath);
+    if (entries.length > 0) return false;
+    rmdirSync(dirPath);
+    return true;
+  } catch {
+    return false;
+  }
+}
 
 // src/hotmemory.ts
 import { existsSync as existsSync2, readFileSync as readFileSync2, writeFileSync as writeFileSync2 } from "fs";
@@ -394,6 +472,25 @@ function decodeToken(token) {
 }
 async function initCommand(opts) {
   const cwd = process.cwd();
+  const ownPkgPath = join3(cwd, "package.json");
+  if (existsSync3(ownPkgPath) && !opts.force) {
+    try {
+      const ownPkg = JSON.parse(readFileSync3(ownPkgPath, "utf8"));
+      if (ownPkg.name === "@cubedot/cli") {
+        console.error(
+          pc.red(
+            "Error: This looks like the Cubedot CLI source repo, not a project to connect.\nRun `cubedot init` inside your target project directory, or pass --force to override."
+          )
+        );
+        process.exit(1);
+      }
+    } catch {
+    }
+  }
+  const claudeMdExisted = existsSync3(join3(cwd, "CLAUDE.md"));
+  const agentsMdExisted = existsSync3(join3(cwd, "AGENTS.md"));
+  const fieldNotesExisted = existsSync3(join3(cwd, ".cubedot", "field-notes.md"));
+  const linksJsonExisted = existsSync3(join3(cwd, ".cubedot", "links.json"));
   let projectId;
   let key;
   let mcpUrl;
@@ -483,7 +580,7 @@ async function initCommand(opts) {
     await client.close();
   }
   writeMcpJson(cwd, mcpUrl, projectId, key);
-  enableMcpServerInSettings(cwd);
+  const { created: settingsCreated } = enableMcpServerInSettings(cwd);
   writeCubedotConfig(cwd, {
     projectId,
     mcpUrl,
@@ -496,7 +593,33 @@ async function initCommand(opts) {
   generateMemoryFiles(cwd, identity, conventions, registry);
   installAgentAssets(cwd);
   scaffoldCubedotDirs(cwd);
-  updateGitignore(cwd);
+  const gitignoreAdded = updateGitignore(cwd);
+  const manifest = {
+    cliVersion: pkg.version,
+    at: (/* @__PURE__ */ new Date()).toISOString(),
+    createdFiles: [
+      ".mcp.json",
+      ".cubedot/config.json",
+      ".cubedot/fia-operating-manual.md",
+      ".claude/agents/CubedotVerifier.md",
+      ...!fieldNotesExisted ? [".cubedot/field-notes.md"] : [],
+      ...!linksJsonExisted ? [".cubedot/links.json"] : []
+    ],
+    createdDirs: [
+      ".cubedot/progress",
+      ".cubedot/reports",
+      ".cubedot/docs",
+      ".cubedot/sync",
+      ".cubedot",
+      ".claude/agents",
+      ".claude"
+    ],
+    claudeMd: claudeMdExisted ? "inserted" : "created",
+    agentsMd: agentsMdExisted ? "inserted" : "created",
+    settingsCreated,
+    gitignoreAdded
+  };
+  writeInstallManifest(cwd, manifest);
   const projectName = orientText.split("\n").find((l) => l.trim())?.replace(/^#+\s*/, "") ?? projectId;
   console.log("\n" + pc.green("\u2713") + " Cubedot connected: " + pc.bold(projectName));
   console.log(pc.dim(`  Project ID : ${projectId}`));
@@ -508,6 +631,8 @@ async function initCommand(opts) {
   const written = [
     ".mcp.json (gitignored \u2014 holds your key)",
     ".cubedot/config.json (gitignored)",
+    ".cubedot/install-manifest.json",
+    ".claude/settings.json (enabledMcpjsonServers)",
     "AGENTS.md",
     "CLAUDE.md",
     ".claude/agents/CubedotVerifier.md",
@@ -521,24 +646,224 @@ async function initCommand(opts) {
   console.log("\nOpen Claude Code in this directory to start building. \u2728");
 }
 
-// src/commands/sync.ts
+// src/commands/uninstall.ts
 import pc2 from "picocolors";
+import { existsSync as existsSync4, readFileSync as readFileSync4, rmSync as rmSync2, unlinkSync as unlinkSync2 } from "fs";
+import { join as join4 } from "path";
+async function uninstallCommand(opts) {
+  const cwd = process.cwd();
+  const hasCubedot = existsSync4(join4(cwd, ".mcp.json")) || existsSync4(join4(cwd, ".cubedot")) || existsSync4(join4(cwd, ".claude", "agents", "CubedotVerifier.md"));
+  if (!hasCubedot) {
+    console.log("Nothing to uninstall here.");
+    return;
+  }
+  const manifest = readInstallManifest(cwd);
+  if (manifest) {
+    await runManifestUninstall(cwd, manifest, opts.yes ?? false);
+  } else {
+    await runHeuristicUninstall(cwd, opts.yes ?? false);
+  }
+}
+async function confirm(skipConfirm) {
+  if (skipConfirm) return true;
+  if (!process.stdin.isTTY) {
+    console.error(pc2.red("Non-interactive shell: pass --yes / -y to skip confirmation."));
+    process.exit(1);
+  }
+  const { default: input } = await import("@inquirer/input");
+  const answer = await input({ message: "Continue? [y/N]" });
+  return answer.trim().toLowerCase() === "y";
+}
+function execute(actions) {
+  for (const a of actions) {
+    try {
+      a.fn();
+    } catch (err) {
+      console.warn(pc2.yellow(`  \u26A0  Could not complete "${a.desc}": ${err.message}`));
+    }
+  }
+}
+async function runManifestUninstall(cwd, manifest, skipConfirm) {
+  const actions = [];
+  for (const rel of manifest.createdFiles) {
+    const abs = join4(cwd, rel);
+    if (existsSync4(abs)) {
+      actions.push({ desc: `delete ${rel}`, fn: () => unlinkSync2(abs) });
+    }
+  }
+  const claudePath = join4(cwd, "CLAUDE.md");
+  if (existsSync4(claudePath)) {
+    if (manifest.claudeMd === "created") {
+      actions.push({
+        desc: "delete CLAUDE.md (created by cubedot init)",
+        fn: () => unlinkSync2(claudePath)
+      });
+    } else {
+      actions.push({
+        desc: "CLAUDE.md \u2014 remove CUBEDOT marker blocks (preserves your content)",
+        fn: () => stripCubedotMarkers(claudePath)
+      });
+    }
+  }
+  const agentsPath = join4(cwd, "AGENTS.md");
+  if (existsSync4(agentsPath)) {
+    if (manifest.agentsMd === "created") {
+      actions.push({
+        desc: "delete AGENTS.md (created by cubedot init)",
+        fn: () => unlinkSync2(agentsPath)
+      });
+    } else {
+      actions.push({
+        desc: "AGENTS.md \u2014 remove CUBEDOT marker blocks (preserves your content)",
+        fn: () => stripCubedotMarkers(agentsPath)
+      });
+    }
+  }
+  const settingsPath = join4(cwd, ".claude", "settings.json");
+  if (existsSync4(settingsPath)) {
+    if (manifest.settingsCreated) {
+      actions.push({
+        desc: "delete .claude/settings.json (created by cubedot init)",
+        fn: () => unlinkSync2(settingsPath)
+      });
+    } else {
+      actions.push({
+        desc: '.claude/settings.json \u2014 remove "cubedot" from enabledMcpjsonServers',
+        fn: () => removeCubedotFromSettings(cwd)
+      });
+    }
+  }
+  if (manifest.gitignoreAdded.length > 0 && existsSync4(join4(cwd, ".gitignore"))) {
+    actions.push({
+      desc: `.gitignore \u2014 remove lines: ${manifest.gitignoreAdded.join(", ")}`,
+      fn: () => stripGitignoreLines(cwd, manifest.gitignoreAdded)
+    });
+  }
+  const manifestAbs = join4(cwd, MANIFEST_PATH);
+  if (existsSync4(manifestAbs)) {
+    actions.push({
+      desc: `delete ${MANIFEST_PATH}`,
+      fn: () => unlinkSync2(manifestAbs)
+    });
+  }
+  if (actions.length === 0) {
+    console.log("Nothing to uninstall here.");
+    return;
+  }
+  printPlan(actions, true);
+  if (!await confirm(skipConfirm)) {
+    console.log("Aborted.");
+    return;
+  }
+  execute(actions);
+  const dirsToTry = [...manifest.createdDirs].reverse();
+  for (const rel of dirsToTry) {
+    tryRmdir(join4(cwd, rel));
+  }
+  console.log("\n" + pc2.green("\u2713") + " Uninstall complete. This folder is no longer connected to Cubedot.");
+}
+async function runHeuristicUninstall(cwd, skipConfirm) {
+  const actions = [];
+  const mcpPath = join4(cwd, ".mcp.json");
+  if (existsSync4(mcpPath)) {
+    actions.push({ desc: "delete .mcp.json", fn: () => unlinkSync2(mcpPath) });
+  }
+  const cubedotDir = join4(cwd, ".cubedot");
+  if (existsSync4(cubedotDir)) {
+    actions.push({
+      desc: "delete .cubedot/ (entire directory)",
+      fn: () => rmSync2(cubedotDir, { recursive: true, force: true })
+    });
+  }
+  const verifierPath = join4(cwd, ".claude", "agents", "CubedotVerifier.md");
+  if (existsSync4(verifierPath)) {
+    actions.push({
+      desc: "delete .claude/agents/CubedotVerifier.md",
+      fn: () => unlinkSync2(verifierPath)
+    });
+  }
+  const settingsPath = join4(cwd, ".claude", "settings.json");
+  if (existsSync4(settingsPath)) {
+    actions.push({
+      desc: '.claude/settings.json \u2014 remove "cubedot" from enabledMcpjsonServers',
+      fn: () => removeCubedotFromSettings(cwd)
+    });
+  }
+  const gitignorePath = join4(cwd, ".gitignore");
+  if (existsSync4(gitignorePath)) {
+    const content = readFileSync4(gitignorePath, "utf8");
+    const lines = content.split("\n");
+    if (GITIGNORE_ENTRIES.some((e) => lines.some((l) => l.trim() === e))) {
+      actions.push({
+        desc: ".gitignore \u2014 remove cubedot lines",
+        fn: () => stripGitignoreLines(cwd, GITIGNORE_ENTRIES)
+      });
+    }
+  }
+  const claudePath = join4(cwd, "CLAUDE.md");
+  if (existsSync4(claudePath)) {
+    const content = readFileSync4(claudePath, "utf8");
+    if (content.includes("<!-- CUBEDOT:START:")) {
+      actions.push({
+        desc: "delete CLAUDE.md (contains cubedot markers \u2014 treated as generated)",
+        fn: () => unlinkSync2(claudePath)
+      });
+    }
+  }
+  const agentsPath = join4(cwd, "AGENTS.md");
+  if (existsSync4(agentsPath)) {
+    const content = readFileSync4(agentsPath, "utf8");
+    if (content.includes("<!-- CUBEDOT:START:")) {
+      actions.push({
+        desc: "delete AGENTS.md (contains cubedot markers \u2014 treated as generated)",
+        fn: () => unlinkSync2(agentsPath)
+      });
+    }
+  }
+  if (actions.length === 0) {
+    console.log("Nothing to uninstall here.");
+    return;
+  }
+  printPlan(actions, false);
+  if (!await confirm(skipConfirm)) {
+    console.log("Aborted.");
+    return;
+  }
+  execute(actions);
+  tryRmdir(join4(cwd, ".claude", "agents"));
+  tryRmdir(join4(cwd, ".claude"));
+  console.log("\n" + pc2.green("\u2713") + " Uninstall complete. This folder is no longer connected to Cubedot.");
+}
+function printPlan(actions, hasManifest) {
+  const mode = hasManifest ? "manifest-based (precise)" : "heuristic (no manifest found)";
+  console.log(pc2.bold(`
+Cubedot uninstall \u2014 ${mode}
+`));
+  console.log("The following changes will be made:\n");
+  for (const a of actions) {
+    console.log("  " + pc2.dim("\u2022") + " " + a.desc);
+  }
+  console.log("");
+}
+
+// src/commands/sync.ts
+import pc3 from "picocolors";
 import { createHash } from "crypto";
-import { existsSync as existsSync5, readFileSync as readFileSync5 } from "fs";
-import { join as join5 } from "path";
+import { existsSync as existsSync6, readFileSync as readFileSync6 } from "fs";
+import { join as join6 } from "path";
 import { fileURLToPath as fileURLToPath3 } from "url";
 import { dirname as dirname3 } from "path";
 
 // src/ledger.ts
 import {
-  existsSync as existsSync4,
+  existsSync as existsSync5,
   mkdirSync as mkdirSync2,
-  readFileSync as readFileSync4,
-  readdirSync,
+  readFileSync as readFileSync5,
+  readdirSync as readdirSync2,
   renameSync,
   writeFileSync as writeFileSync3
 } from "fs";
-import { join as join4 } from "path";
+import { join as join5 } from "path";
 import { randomUUID } from "crypto";
 var FN_CODE_REGEX = /^FN-\d{3}-\d{2,}$/;
 function validateFnCode(code) {
@@ -549,13 +874,13 @@ function validateFnCode(code) {
   }
 }
 function getLedgerPath(cwd, code) {
-  return join4(cwd, ".cubedot", "progress", `${code}.json`);
+  return join5(cwd, ".cubedot", "progress", `${code}.json`);
 }
 function readLedger(cwd, code) {
   const path = getLedgerPath(cwd, code);
-  if (!existsSync4(path)) return null;
+  if (!existsSync5(path)) return null;
   try {
-    return JSON.parse(readFileSync4(path, "utf8"));
+    return JSON.parse(readFileSync5(path, "utf8"));
   } catch {
     throw new Error(
       `Failed to read ledger for ${code}: file exists but contains malformed JSON.`
@@ -563,11 +888,11 @@ function readLedger(cwd, code) {
   }
 }
 function readAllLedgers(cwd) {
-  const dir = join4(cwd, ".cubedot", "progress");
-  if (!existsSync4(dir)) return [];
-  return readdirSync(dir).filter((f) => f.endsWith(".json")).map((f) => {
+  const dir = join5(cwd, ".cubedot", "progress");
+  if (!existsSync5(dir)) return [];
+  return readdirSync2(dir).filter((f) => f.endsWith(".json")).map((f) => {
     try {
-      return JSON.parse(readFileSync4(join4(dir, f), "utf8"));
+      return JSON.parse(readFileSync5(join5(dir, f), "utf8"));
     } catch {
       return null;
     }
@@ -575,8 +900,8 @@ function readAllLedgers(cwd) {
 }
 function writeLedger(cwd, record) {
   const path = getLedgerPath(cwd, record.code);
-  const dir = join4(cwd, ".cubedot", "progress");
-  if (!existsSync4(dir)) mkdirSync2(dir, { recursive: true });
+  const dir = join5(cwd, ".cubedot", "progress");
+  if (!existsSync5(dir)) mkdirSync2(dir, { recursive: true });
   const tmp = `${path}.${randomUUID()}.tmp`;
   writeFileSync3(tmp, JSON.stringify(record, null, 2) + "\n", "utf8");
   renameSync(tmp, path);
@@ -669,12 +994,12 @@ function doneFn(cwd, code, actor = "human", force = false, discrepancies = []) {
 var __filename2 = fileURLToPath3(import.meta.url);
 var __dirname3 = dirname3(__filename2);
 var pkg2 = JSON.parse(
-  readFileSync5(join5(__dirname3, "../package.json"), "utf8")
+  readFileSync6(join6(__dirname3, "../package.json"), "utf8")
 );
 function fileHash(filePath) {
-  if (!existsSync5(filePath)) return "";
+  if (!existsSync6(filePath)) return "";
   try {
-    return createHash("sha256").update(readFileSync5(filePath)).digest("hex");
+    return createHash("sha256").update(readFileSync6(filePath)).digest("hex");
   } catch {
     return "";
   }
@@ -684,7 +1009,7 @@ async function syncCommand() {
   const config = readCubedotConfig(cwd);
   if (!config) {
     console.error(
-      pc2.red(
+      pc3.red(
         "Error: .cubedot/config.json not found. Run `cubedot init` first."
       )
     );
@@ -695,26 +1020,26 @@ async function syncCommand() {
     const ageDays = (Date.now() - new Date(config.lastSynced).getTime()) / 864e5;
     if (ageDays >= STALE_DAYS) {
       console.log(
-        pc2.yellow(
+        pc3.yellow(
           `\u26A0  Last synced ${Math.floor(ageDays)} day(s) ago \u2014 refreshing now.`
         )
       );
     }
   }
   const connectUrl = buildConnectUrl(config.mcpUrl, config.projectId);
-  console.log(pc2.dim(`Connecting to ${connectUrl} \u2026`));
+  console.log(pc3.dim(`Connecting to ${connectUrl} \u2026`));
   let client;
   try {
     client = await createMcpClient(connectUrl, await readKeyFromMcpJson(cwd));
   } catch (err) {
-    console.error(pc2.red(`Error: ${categorizeError(err)}`));
+    console.error(pc3.red(`Error: ${categorizeError(err)}`));
     process.exit(1);
   }
   try {
     await validateTools(client);
   } catch (err) {
     await client.close();
-    console.error(pc2.red(`Error: ${err.message}`));
+    console.error(pc3.red(`Error: ${err.message}`));
     process.exit(1);
   }
   let orientText = "";
@@ -732,7 +1057,7 @@ async function syncCommand() {
   } catch (err) {
     await client.close();
     console.error(
-      pc2.red(`Error fetching project data: ${err.message}`)
+      pc3.red(`Error fetching project data: ${err.message}`)
     );
     process.exit(1);
   } finally {
@@ -759,7 +1084,7 @@ async function syncCommand() {
   const skipOrphanDetection = specFnCodes.size === 0 && ledgers.length > 0;
   if (skipOrphanDetection) {
     console.log(
-      pc2.yellow(
+      pc3.yellow(
         "\u26A0  Spec tree returned no functionalities \u2014 skipping orphan detection this sync."
       )
     );
@@ -775,7 +1100,7 @@ async function syncCommand() {
     if (record.state === "done") {
       const files = links[record.code] ?? [];
       for (const filePath of files) {
-        const absPath = join5(cwd, filePath);
+        const absPath = join6(cwd, filePath);
         const newHash = fileHash(absPath);
         const oldHash = prevHashes[filePath] ?? "";
         nextHashes[filePath] = newHash;
@@ -793,35 +1118,35 @@ async function syncCommand() {
   }
   for (const [code, files] of Object.entries(links)) {
     for (const filePath of files) {
-      const absPath = join5(cwd, filePath);
+      const absPath = join6(cwd, filePath);
       nextHashes[filePath] = fileHash(absPath);
     }
   }
   writeHashes(cwd, nextHashes);
-  console.log(pc2.green("\u2713") + " Sync complete.");
+  console.log(pc3.green("\u2713") + " Sync complete.");
   if (orphaned.length > 0) {
     console.log(
-      pc2.yellow(`  Orphaned (removed from spec): ${orphaned.join(", ")}`)
+      pc3.yellow(`  Orphaned (removed from spec): ${orphaned.join(", ")}`)
     );
   }
   if (needsReverification.length > 0) {
     console.log(
-      pc2.yellow(
+      pc3.yellow(
         `  Needs re-verification (spec changed after done): ${needsReverification.join(", ")}`
       )
     );
   }
   if (orphaned.length === 0 && needsReverification.length === 0) {
-    console.log(pc2.dim("  No drift detected."));
+    console.log(pc3.dim("  No drift detected."));
   }
-  console.log(pc2.dim("  AGENTS.md and CLAUDE.md updated."));
+  console.log(pc3.dim("  AGENTS.md and CLAUDE.md updated."));
 }
 async function readKeyFromMcpJson(cwd) {
-  const mcpPath = join5(cwd, ".mcp.json");
-  if (!existsSync5(mcpPath)) {
+  const mcpPath = join6(cwd, ".mcp.json");
+  if (!existsSync6(mcpPath)) {
     throw new Error(".mcp.json not found. Run `cubedot init` first.");
   }
-  const mcp = JSON.parse(readFileSync5(mcpPath, "utf8"));
+  const mcp = JSON.parse(readFileSync6(mcpPath, "utf8"));
   const headers = mcp.mcpServers?.["cubedot"]?.headers ?? {};
   const authHeader = headers["Authorization"] ?? headers["authorization"] ?? "";
   const key = authHeader.replace(/^ApiKey\s+/i, "").trim();
@@ -834,90 +1159,90 @@ async function readKeyFromMcpJson(cwd) {
 }
 
 // src/commands/status.ts
-import pc3 from "picocolors";
-import { existsSync as existsSync6, readFileSync as readFileSync6 } from "fs";
-import { join as join6 } from "path";
+import pc4 from "picocolors";
+import { existsSync as existsSync7, readFileSync as readFileSync7 } from "fs";
+import { join as join7 } from "path";
 async function statusCommand() {
   const cwd = process.cwd();
   let ok = true;
   const config = readCubedotConfig(cwd);
   if (!config) {
-    console.log(pc3.red("\u2717") + " .cubedot/config.json \u2014 missing (run `cubedot init`)");
+    console.log(pc4.red("\u2717") + " .cubedot/config.json \u2014 missing (run `cubedot init`)");
     ok = false;
   } else {
-    console.log(pc3.green("\u2713") + " .cubedot/config.json");
-    console.log(pc3.dim(`    projectId: ${config.projectId}`));
+    console.log(pc4.green("\u2713") + " .cubedot/config.json");
+    console.log(pc4.dim(`    projectId: ${config.projectId}`));
     if (config.lastSynced) {
       const ageDays = (Date.now() - new Date(config.lastSynced).getTime()) / 864e5;
       const ageStr = ageDays < 1 ? "today" : `${Math.floor(ageDays)} day(s) ago`;
       const stale = ageDays >= 3;
       console.log(
-        (stale ? pc3.yellow("\u26A0 ") : pc3.dim("   ")) + `  Last synced: ${ageStr}${stale ? " \u2014 consider running `cubedot sync`" : ""}`
+        (stale ? pc4.yellow("\u26A0 ") : pc4.dim("   ")) + `  Last synced: ${ageStr}${stale ? " \u2014 consider running `cubedot sync`" : ""}`
       );
     }
   }
-  const mcpPath = join6(cwd, ".mcp.json");
-  if (!existsSync6(mcpPath)) {
-    console.log(pc3.red("\u2717") + " .mcp.json \u2014 missing");
+  const mcpPath = join7(cwd, ".mcp.json");
+  if (!existsSync7(mcpPath)) {
+    console.log(pc4.red("\u2717") + " .mcp.json \u2014 missing");
     ok = false;
   } else {
     try {
-      const mcp = JSON.parse(readFileSync6(mcpPath, "utf8"));
+      const mcp = JSON.parse(readFileSync7(mcpPath, "utf8"));
       const headers = mcp.mcpServers?.["cubedot"]?.headers ?? {};
       const authHeader = headers["Authorization"] ?? headers["authorization"] ?? "";
       const keyRaw = authHeader.replace(/^ApiKey\s+/i, "").trim();
       const keyTail = keyRaw ? keyRaw.slice(-8) : "(empty)";
-      console.log(pc3.green("\u2713") + ` .mcp.json \u2014 key tail: \u2026${keyTail}`);
+      console.log(pc4.green("\u2713") + ` .mcp.json \u2014 key tail: \u2026${keyTail}`);
     } catch {
-      console.log(pc3.red("\u2717") + " .mcp.json \u2014 malformed JSON");
+      console.log(pc4.red("\u2717") + " .mcp.json \u2014 malformed JSON");
       ok = false;
     }
   }
   for (const file of ["AGENTS.md", "CLAUDE.md"]) {
-    const path = join6(cwd, file);
-    if (!existsSync6(path)) {
-      console.log(pc3.red("\u2717") + ` ${file} \u2014 missing`);
+    const path = join7(cwd, file);
+    if (!existsSync7(path)) {
+      console.log(pc4.red("\u2717") + ` ${file} \u2014 missing`);
       ok = false;
     } else {
-      const content = readFileSync6(path, "utf8");
+      const content = readFileSync7(path, "utf8");
       const markers = hasAllMarkers(content);
       console.log(
-        (markers ? pc3.green("\u2713") : pc3.yellow("\u26A0")) + ` ${file}${markers ? "" : " \u2014 markers missing or malformed (run `cubedot sync`)"}`
+        (markers ? pc4.green("\u2713") : pc4.yellow("\u26A0")) + ` ${file}${markers ? "" : " \u2014 markers missing or malformed (run `cubedot sync`)"}`
       );
     }
   }
-  const verifier = join6(cwd, ".claude", "agents", "CubedotVerifier.md");
-  const manual = join6(cwd, ".cubedot", "fia-operating-manual.md");
+  const verifier = join7(cwd, ".claude", "agents", "CubedotVerifier.md");
+  const manual = join7(cwd, ".cubedot", "fia-operating-manual.md");
   console.log(
-    (existsSync6(verifier) ? pc3.green("\u2713") : pc3.red("\u2717")) + " .claude/agents/CubedotVerifier.md"
+    (existsSync7(verifier) ? pc4.green("\u2713") : pc4.red("\u2717")) + " .claude/agents/CubedotVerifier.md"
   );
   console.log(
-    (existsSync6(manual) ? pc3.green("\u2713") : pc3.red("\u2717")) + " .cubedot/fia-operating-manual.md"
+    (existsSync7(manual) ? pc4.green("\u2713") : pc4.red("\u2717")) + " .cubedot/fia-operating-manual.md"
   );
   const ledgers = readAllLedgers(cwd);
   if (ledgers.length === 0) {
-    console.log(pc3.dim("  Ledger: no entries yet"));
+    console.log(pc4.dim("  Ledger: no entries yet"));
   } else {
     const counts = {};
     for (const l of ledgers) counts[l.state] = (counts[l.state] ?? 0) + 1;
     const summary = Object.entries(counts).map(([s, n]) => `${n} ${s}`).join(", ");
-    console.log(pc3.dim(`  Ledger: ${ledgers.length} entries (${summary})`));
+    console.log(pc4.dim(`  Ledger: ${ledgers.length} entries (${summary})`));
   }
   if (config) {
-    console.log(pc3.dim("\nChecking MCP connectivity \u2026"));
+    console.log(pc4.dim("\nChecking MCP connectivity \u2026"));
     try {
       const key = await readKeyFromMcpJson(cwd);
       const connectUrl = buildConnectUrl(config.mcpUrl, config.projectId);
       const client = await createMcpClient(connectUrl, key);
       try {
         await validateTools(client);
-        console.log(pc3.green("\u2713") + " MCP server reachable \u2014 all 7 tools present");
+        console.log(pc4.green("\u2713") + " MCP server reachable \u2014 all 7 tools present");
       } finally {
         await client.close();
       }
     } catch (err) {
       console.log(
-        pc3.red("\u2717") + " MCP server: " + categorizeError(err)
+        pc4.red("\u2717") + " MCP server: " + categorizeError(err)
       );
       ok = false;
     }
@@ -926,9 +1251,9 @@ async function statusCommand() {
 }
 
 // src/commands/check.ts
-import pc4 from "picocolors";
-import { existsSync as existsSync7, readFileSync as readFileSync7 } from "fs";
-import { join as join7 } from "path";
+import pc5 from "picocolors";
+import { existsSync as existsSync8, readFileSync as readFileSync8 } from "fs";
+import { join as join8 } from "path";
 async function checkCommand() {
   const cwd = process.cwd();
   const issues = [];
@@ -936,12 +1261,12 @@ async function checkCommand() {
   if (!config) {
     issues.push(".cubedot/config.json missing \u2014 run `cubedot init`");
   }
-  const mcpPath = join7(cwd, ".mcp.json");
-  if (!existsSync7(mcpPath)) {
+  const mcpPath = join8(cwd, ".mcp.json");
+  if (!existsSync8(mcpPath)) {
     issues.push(".mcp.json missing \u2014 run `cubedot init`");
   } else {
     try {
-      const mcp = JSON.parse(readFileSync7(mcpPath, "utf8"));
+      const mcp = JSON.parse(readFileSync8(mcpPath, "utf8"));
       if (!mcp.mcpServers?.["cubedot"]) {
         issues.push(
           ".mcp.json missing mcpServers.cubedot \u2014 run `cubedot init`"
@@ -951,106 +1276,106 @@ async function checkCommand() {
       issues.push(".mcp.json contains malformed JSON");
     }
   }
-  const agentsPath = join7(cwd, "AGENTS.md");
-  if (!existsSync7(agentsPath)) {
+  const agentsPath = join8(cwd, "AGENTS.md");
+  if (!existsSync8(agentsPath)) {
     issues.push("AGENTS.md missing \u2014 run `cubedot init`");
   } else {
-    const content = readFileSync7(agentsPath, "utf8");
+    const content = readFileSync8(agentsPath, "utf8");
     if (!hasAllMarkers(content)) {
       issues.push(
         "AGENTS.md is missing or has malformed CUBEDOT markers \u2014 run `cubedot sync`"
       );
     }
   }
-  const claudePath = join7(cwd, "CLAUDE.md");
-  if (!existsSync7(claudePath)) {
+  const claudePath = join8(cwd, "CLAUDE.md");
+  if (!existsSync8(claudePath)) {
     issues.push("CLAUDE.md missing \u2014 run `cubedot init`");
   } else {
-    const content = readFileSync7(claudePath, "utf8");
+    const content = readFileSync8(claudePath, "utf8");
     if (!hasAllMarkers(content)) {
       issues.push(
         "CLAUDE.md is missing or has malformed CUBEDOT markers \u2014 run `cubedot sync`"
       );
     }
   }
-  const verifier = join7(cwd, ".claude", "agents", "CubedotVerifier.md");
-  if (!existsSync7(verifier)) {
+  const verifier = join8(cwd, ".claude", "agents", "CubedotVerifier.md");
+  if (!existsSync8(verifier)) {
     issues.push(
       ".claude/agents/CubedotVerifier.md missing \u2014 run `cubedot init`"
     );
   }
-  const manual = join7(cwd, ".cubedot", "fia-operating-manual.md");
-  if (!existsSync7(manual)) {
+  const manual = join8(cwd, ".cubedot", "fia-operating-manual.md");
+  if (!existsSync8(manual)) {
     issues.push(
       ".cubedot/fia-operating-manual.md missing \u2014 run `cubedot init`"
     );
   }
   for (const dir of [".cubedot/progress", ".cubedot/reports"]) {
-    if (!existsSync7(join7(cwd, dir))) {
+    if (!existsSync8(join8(cwd, dir))) {
       issues.push(`${dir}/ missing \u2014 run 'cubedot init'`);
     }
   }
-  if (existsSync7(claudePath)) {
-    const content = readFileSync7(claudePath, "utf8");
-    if (content.includes("fia-operating-manual") && !existsSync7(join7(cwd, ".cubedot", "fia-operating-manual.md"))) {
+  if (existsSync8(claudePath)) {
+    const content = readFileSync8(claudePath, "utf8");
+    if (content.includes("fia-operating-manual") && !existsSync8(join8(cwd, ".cubedot", "fia-operating-manual.md"))) {
       issues.push(
         "CLAUDE.md references .cubedot/fia-operating-manual.md but it is missing"
       );
     }
   }
   if (issues.length === 0) {
-    console.log(pc4.green("\u2713") + " All checks passed.");
+    console.log(pc5.green("\u2713") + " All checks passed.");
     process.exit(0);
   } else {
-    console.log(pc4.red(`\u2717 ${issues.length} issue(s) found:
+    console.log(pc5.red(`\u2717 ${issues.length} issue(s) found:
 `));
     for (const issue of issues) {
-      console.log("  " + pc4.red("\u2022") + " " + issue);
+      console.log("  " + pc5.red("\u2022") + " " + issue);
     }
     process.exit(1);
   }
 }
 
 // src/commands/start.ts
-import pc5 from "picocolors";
+import pc6 from "picocolors";
 function startCommand(fn, opts) {
   const cwd = process.cwd();
   const actor = opts.actor === "human" ? "human" : "agent";
   try {
     const record = startFn(cwd, fn, actor);
     console.log(
-      pc5.green("\u2713") + ` ${fn} \u2192 in_progress (actor: ${record.actor}, at: ${record.updatedAt})`
+      pc6.green("\u2713") + ` ${fn} \u2192 in_progress (actor: ${record.actor}, at: ${record.updatedAt})`
     );
-    console.log(pc5.dim(`  Ledger: .cubedot/progress/${fn}.json`));
+    console.log(pc6.dim(`  Ledger: .cubedot/progress/${fn}.json`));
   } catch (err) {
-    console.error(pc5.red(`Error: ${err.message}`));
+    console.error(pc6.red(`Error: ${err.message}`));
     process.exit(1);
   }
 }
 
 // src/commands/complete.ts
-import pc6 from "picocolors";
+import pc7 from "picocolors";
 function completeCommand(fn, opts) {
   const cwd = process.cwd();
   const actor = opts.actor === "human" ? "human" : "agent";
   try {
     const record = completeFn(cwd, fn, actor);
     console.log(
-      pc6.green("\u2713") + ` ${fn} \u2192 code-complete (actor: ${record.actor}, at: ${record.updatedAt})`
+      pc7.green("\u2713") + ` ${fn} \u2192 code-complete (actor: ${record.actor}, at: ${record.updatedAt})`
     );
     console.log(
-      pc6.dim(
+      pc7.dim(
         `  Next: spawn CubedotVerifier, then ask the developer to run \`cubedot done ${fn}\`.`
       )
     );
   } catch (err) {
-    console.error(pc6.red(`Error: ${err.message}`));
+    console.error(pc7.red(`Error: ${err.message}`));
     process.exit(1);
   }
 }
 
 // src/commands/done.ts
-import pc7 from "picocolors";
+import pc8 from "picocolors";
 function doneCommand(fn, opts) {
   const cwd = process.cwd();
   const actor = opts.actor === "agent" ? "agent" : "human";
@@ -1062,43 +1387,43 @@ function doneCommand(fn, opts) {
   try {
     const record = doneFn(cwd, fn, actor, force, discrepancies);
     console.log(
-      pc7.green("\u2713") + ` ${fn} \u2192 done (actor: ${record.actor}, at: ${record.updatedAt})`
+      pc8.green("\u2713") + ` ${fn} \u2192 done (actor: ${record.actor}, at: ${record.updatedAt})`
     );
     if (record.overrides.length > 0) {
       console.log(
-        pc7.yellow(
+        pc8.yellow(
           `  \u26A0  Override recorded: ${record.overrides[record.overrides.length - 1].condition}`
         )
       );
     }
     if (discrepancies.length > 0) {
       console.log(
-        pc7.yellow(
+        pc8.yellow(
           `  \u26A0  ${discrepancies.length} discrepancy(ies) recorded (criteria accepted unmet):`
         )
       );
       for (const d of discrepancies) {
-        console.log(pc7.yellow(`     - ${d.criterion}`));
+        console.log(pc8.yellow(`     - ${d.criterion}`));
       }
     }
   } catch (err) {
-    console.error(pc7.red(`Error: ${err.message}`));
+    console.error(pc8.red(`Error: ${err.message}`));
     process.exit(1);
   }
 }
 
 // src/commands/progress.ts
-import pc8 from "picocolors";
-import { existsSync as existsSync8, readFileSync as readFileSync8 } from "fs";
-import { join as join8 } from "path";
+import pc9 from "picocolors";
+import { existsSync as existsSync9, readFileSync as readFileSync9 } from "fs";
+import { join as join9 } from "path";
 function progressCommand() {
   const cwd = process.cwd();
   const ledgers = readAllLedgers(cwd);
   let fnNames = /* @__PURE__ */ new Map();
   for (const file of ["AGENTS.md", "CLAUDE.md"]) {
-    const path = join8(cwd, file);
-    if (existsSync8(path)) {
-      fnNames = parseRegistryBlock(readFileSync8(path, "utf8"));
+    const path = join9(cwd, file);
+    if (existsSync9(path)) {
+      fnNames = parseRegistryBlock(readFileSync9(path, "utf8"));
       if (fnNames.size > 0) break;
     }
   }
@@ -1117,24 +1442,24 @@ function progressCommand() {
   const ccCount = byState["code-complete"].length;
   const ipCount = byState["in_progress"].length;
   const todoCount = Math.max(0, total - doneCount - ccCount - ipCount);
-  console.log("\n" + pc8.bold("Progress Summary"));
+  console.log("\n" + pc9.bold("Progress Summary"));
   console.log("\u2501".repeat(40));
-  console.log(`  Done:           ${pc8.green(String(doneCount))}/${total}`);
+  console.log(`  Done:           ${pc9.green(String(doneCount))}/${total}`);
   if (ccCount > 0)
-    console.log(`  Code-complete:  ${pc8.cyan(String(ccCount))}/${total}`);
+    console.log(`  Code-complete:  ${pc9.cyan(String(ccCount))}/${total}`);
   if (ipCount > 0)
-    console.log(`  In progress:    ${pc8.yellow(String(ipCount))}/${total}`);
+    console.log(`  In progress:    ${pc9.yellow(String(ipCount))}/${total}`);
   if (todoCount > 0)
-    console.log(`  Todo:           ${pc8.dim(String(todoCount))}/${total}`);
+    console.log(`  Todo:           ${pc9.dim(String(todoCount))}/${total}`);
   const active = [
     ...byState["in_progress"],
     ...byState["code-complete"]
   ];
   if (active.length > 0) {
-    console.log("\n" + pc8.bold("Active:"));
+    console.log("\n" + pc9.bold("Active:"));
     for (const l of active) {
       const name = fnNames.get(l.code) ? ` \u2014 ${fnNames.get(l.code)}` : "";
-      const stateLabel = l.state === "in_progress" ? pc8.yellow("in_progress") : pc8.cyan("code-complete");
+      const stateLabel = l.state === "in_progress" ? pc9.yellow("in_progress") : pc9.cyan("code-complete");
       console.log(`  ${l.code}${name}  [${stateLabel}]`);
     }
   }
@@ -1143,21 +1468,21 @@ function progressCommand() {
     const registryOrder = Array.from(fnNames.keys());
     const nextCode = registryOrder.find((code) => !ledgerCodes.has(code));
     if (nextCode) {
-      console.log("\n" + pc8.bold("Next unblocked:"));
+      console.log("\n" + pc9.bold("Next unblocked:"));
       console.log(`  ${nextCode} \u2014 ${fnNames.get(nextCode) ?? ""}`);
     }
   }
   if (flagged.length > 0) {
-    console.log("\n" + pc8.bold(pc8.yellow("Flagged:")));
+    console.log("\n" + pc9.bold(pc9.yellow("Flagged:")));
     for (const l of flagged) {
       console.log(`  ${l.code}  [${l.flags.join(", ")}]`);
     }
   }
   if (byState["done"].length > 0) {
-    console.log("\n" + pc8.bold("Done:"));
+    console.log("\n" + pc9.bold("Done:"));
     for (const l of byState["done"]) {
       const name = fnNames.get(l.code) ? ` \u2014 ${fnNames.get(l.code)}` : "";
-      console.log(`  ${pc8.green("\u2713")} ${l.code}${name}`);
+      console.log(`  ${pc9.green("\u2713")} ${l.code}${name}`);
     }
   }
   console.log("");
@@ -1167,15 +1492,16 @@ function progressCommand() {
 var __filename3 = fileURLToPath4(import.meta.url);
 var __dirname4 = dirname4(__filename3);
 var pkg3 = JSON.parse(
-  readFileSync9(join9(__dirname4, "../package.json"), "utf8")
+  readFileSync10(join10(__dirname4, "../package.json"), "utf8")
 );
 var program = new Command();
 var collect = (value, prev) => [...prev, value];
 program.name("cubedot").description(
   "Connect your repo to the Cubedot MCP and drive the spec-first build loop."
 ).version(pkg3.version);
-program.command("init").description("Connect and scaffold the repo (validates MCP, writes config + hot-memory files).").option("--token <token>", "Base64url connect token {v:1, projectId, key, mcpUrl}").option("--project <projectId>", "Project ID (alternative to --token)").option("--key <key>", "MCP API key (alternative to --token)").option("--url <url>", "MCP URL (alternative to --token)").action(initCommand);
+program.command("init").description("Connect and scaffold the repo (validates MCP, writes config + hot-memory files).").option("--token <token>", "Base64url connect token {v:1, projectId, key, mcpUrl}").option("--project <projectId>", "Project ID (alternative to --token)").option("--key <key>", "MCP API key (alternative to --token)").option("--url <url>", "MCP URL (alternative to --token)").option("--force", "Override the self-install guard (run init inside the CLI source repo).").action(initCommand);
 program.command("sync").description("Refresh local projection (AGENTS.md/CLAUDE.md markers) and detect drift.").action(syncCommand);
+program.command("uninstall").description("Remove all cubedot scaffold files from this repo and disconnect from the MCP.").option("-y, --yes", "Skip the confirmation prompt.").action(uninstallCommand);
 program.command("status").description("Connectivity ping + file-health check (read-only).").action(statusCommand);
 program.command("check").description("Validate markers, config, and server name (read-only; CI-friendly).").action(checkCommand);
 program.command("start <fn>").description("Set a functionality to in_progress.").option("--actor <actor>", "Actor performing the action", "agent").action(startCommand);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cubedot/cli",
-  "version": "0.1.1",
+  "version": "0.1.3",
   "description": "Cubedot CLI — connect your repo to the Cubedot MCP and drive the build loop",
   "license": "UNLICENSED",
   "homepage": "https://cubedot.ai",