clast-ai 0.2.0 → 0.2.2

package/.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "clast",
-  "version": "0.2.0",
+  "version": "0.2.2",
   "description": "Code index for coding agents: symbol search, exact symbol source, type-aware call graph, references, type hierarchy, change impact, dead code and exact counts for any repository. TypeScript, JavaScript, Python, Java, C#, Go, Rust, C, C++, Ruby, PHP, Swift and Dart.",
   "author": {
     "name": "Thomas"

package/README.md

@@ -51,8 +51,48 @@ and four slash commands:
 | `/clast:audit [path]` | Inventory for due diligence or onboarding: size, structure, endpoints, database access, dependencies, dead code |
 | `/clast:status` | State of the index |
 
-The plugin starts the server from a global `clast-ai` 0.2.x when there is one, otherwise through
-`npx clast-ai@0.2` (downloaded on first use). Update with `/plugin update clast@clast`.
+The plugin starts the server from a global `clast-ai` that is at least as new as the plugin, otherwise
+through `npx clast-ai@<plugin version>` (downloaded on first use).
+
+### Upgrading from an older install
+
+If clast is already set up the old way (`npm install -g clast-ai` plus `claude mcp add`, or through
+the old VS Code extension), install the plugin and restart. That is all, provided Node.js is 22.22 or
+newer (0.1 ran on Node 18; check with `node --version`):
+
+```
+/plugin marketplace add xls/clast
+/plugin install clast@clast
+```
+
+The first session after that cleans up in the background, once per plugin version:
+
+- clast servers registered with `claude mcp add`, for all projects or for single ones, are removed
+  (the plugin provides the server; with both, every tool would be listed twice),
+- entries the old VS Code extension wrote into `.claude/settings.local.json` are removed,
+- the v0.1 index file `.clast/clast.db` is deleted (the new index is rebuilt by itself).
+
+Restart Claude Code once more and `/mcp` shows a single `clast` server.
+
+One case is left to you: a project whose `.mcp.json` lists clast. That file is shared with a team, so
+it is never changed, and in that project the server stays listed twice until the entry is removed
+from the file (`clast-ai migrate` names the file).
+
+Optional: `npm uninstall -g clast-ai` removes the old global package. The plugin does not need it; it
+only uses a global install that is at least as new as the plugin itself.
+
+To see what would be removed, or to do it by hand (for example when you keep using the plain MCP
+server and only want the old index gone):
+
+```bash
+clast-ai migrate           # report only
+clast-ai migrate --apply   # remove the leftovers
+```
+
+What was removed is logged to `migrate.log` in the plugin's data folder. `CLAST_NO_MIGRATE=1` switches
+the automatic clean-up off.
+
+Later plugin updates: `/plugin marketplace update clast`, then `/plugin update clast@clast`.
 
 ### As a plain MCP server
 
@@ -62,7 +102,8 @@ claude mcp add -s user clast clast-ai
 ```
 
 `-s user` registers the server for all projects. This gives the tools without the skill and the slash
-commands. Use one of the two ways, not both: with both, every tool is listed twice.
+commands. Use one of the two ways, not both: with both, every tool is listed twice (the plugin removes
+a registration made this way when it is installed later).
 
 Either way, restart Claude Code (or "Developer: Reload Window" in VS Code) and run `/mcp`: `clast`
 should be listed with 15 tools. The first start indexes the project in the background (seconds, about
@@ -398,6 +439,21 @@ Known limitations).
 
 ## Changelog
 
+### 0.2.2
+
+- The clean-up of older installs also finds servers registered as `node .../dist/server/index.js` (how
+  the 0.1 README registered a build from source) and reads the configuration from `CLAUDE_CONFIG_DIR`
+  when that is set. Both were found by installing the plugin into an empty configuration next to an
+  old-style registration.
+
+### 0.2.1
+
+- `clast-ai migrate`: finds and removes what older installs left behind (duplicate MCP registrations
+  next to the plugin, entries written by the old VS Code extension, the v0.1 index file). The plugin
+  runs it automatically, once per version, at the first session after an install or update.
+- The plugin uses a global `clast-ai` only when it is at least as new as the plugin itself, so a
+  plugin update is not held back by an older global install.
+
 ### 0.2.0
 
 New tools (7 to 13):
@@ -450,7 +506,7 @@ Other:
 
 - Swift and Dart added (14 languages).
 - All dependencies updated (MCP SDK 1.32, web-tree-sitter 0.27).
-- 283 tests, plus `bench/bench.mjs`, `bench/resolution.mjs` and the A/B harness `bench/ab.mjs`.
+- 291 tests, plus `bench/bench.mjs`, `bench/resolution.mjs` and the A/B harness `bench/ab.mjs`.
 - Installable as a Claude Code plugin from this repository (`/plugin marketplace add xls/clast`,
   `/plugin install clast@clast`): the MCP server, a usage skill, and the slash commands
   `/clast:deadcode`, `/clast:impact`, `/clast:audit` and `/clast:status`. The old VS Code extension
@@ -466,10 +522,12 @@ Other:
 
 ### Upgrading from 0.1
 
+How to upgrade: see [Upgrading from an older install](#upgrading-from-an-older-install). What changed:
+
 - Node.js 22.22+ is required (was 18).
 - The index moved from `.clast/clast.db` (sql.js) to `.clast/index.db` (`node:sqlite`). Nothing is
-  migrated: the index is a cache and is rebuilt on first start. The old file is ignored and can be
-  deleted.
+  migrated: the index is a cache and is rebuilt on first start. The old file is ignored; the plugin
+  (or `clast-ai migrate --apply`) deletes it.
 - A later schema change deletes and rebuilds the index automatically (the schema is at version 26).
 - Tool output is compact text instead of JSON.
 - `clast_call_graph` defaults to depth 1 and gained `within` and `includeTests`.

package/dist/cli.js

@@ -33,6 +33,8 @@ usage: clast-ai [command] [args] [--root <dir>]
   unused [path]              dead code   [--kind k] [--lang l] [--limit n] [--no-exported]
   stats [what] [name]        exact counts: inventory | symbols | subtypes | calls | text | imports | endpoints | database
                              [--kind k] [--on receiver] [--path p] [--lang l] [--group-by g] [--depth n] [--limit n] [--tests]
+  migrate [--apply]          find (and with --apply remove) what older installs left behind: duplicate
+                             MCP registrations next to the plugin, the v0.1 index file
   parse <file> [--json]      debug: show what the extractor produces for a file
   ast <file>                 debug: dump the tree-sitter syntax tree
 
@@ -54,7 +56,7 @@ const CLI_NAMES = {
     clast_status: 'clast-ai status',
 };
 const BOOLEAN_FLAGS = new Set([
-    'force', 'json', 'regex', 'no-body', 'no-scan', 'no-tests', 'tests', 'uncertain', 'help', 'version', 'all', 'no-exported',
+    'force', 'json', 'regex', 'no-body', 'no-scan', 'no-tests', 'tests', 'uncertain', 'help', 'version', 'all', 'no-exported', 'apply', 'auto',
 ]);
 function parseArgs(argv) {
     const positional = [];
@@ -100,6 +102,13 @@ async function main() {
         await startServer();
         return;
     }
+    if (cmd === 'migrate') {
+        const { migrate } = await import('./migrate.js');
+        const out = await migrate({ apply: flags.has('apply'), auto: flags.has('auto'), force: flags.has('force'), cwd: str('root') });
+        if (out)
+            console.log(out);
+        return;
+    }
     if (cmd === 'parse' || cmd === 'ast') {
         const file = positional[0];
         if (!file)

package/dist/cli.js.map

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package/dist/migrate.d.ts

@@ -0,0 +1,34 @@
+export interface MigrateOptions {
+    /** Make the changes. Default: only report. */
+    apply?: boolean;
+    /** Run from the plugin at session start: once per version, silent, only when the plugin is installed. */
+    auto?: boolean;
+    /** Remove hand-made registrations even when the plugin is not installed. */
+    force?: boolean;
+    home?: string;
+    cwd?: string;
+    /** Replaces `claude mcp remove` (tests). Returns true on success. */
+    remove?: (name: string, scope: 'user' | 'local', cwd: string) => boolean;
+}
+export type Action = {
+    kind: 'mcp';
+    scope: 'user' | 'local';
+    name: string;
+    dir: string;
+    command: string;
+} | {
+    kind: 'settings';
+    file: string;
+    name: string;
+} | {
+    kind: 'index';
+    files: string[];
+} | {
+    kind: 'shared';
+    file: string;
+    name: string;
+};
+export declare function pluginInstalled(home: string): boolean;
+/** Everything an older install left behind, without changing anything. */
+export declare function planMigration(home: string, cwd: string): Action[];
+export declare function migrate(opts?: MigrateOptions): Promise<string>;

package/dist/migrate.js

@@ -0,0 +1,205 @@
+import { spawnSync } from 'node:child_process';
+import { appendFileSync, existsSync, mkdirSync, readFileSync, rmSync, writeFileSync } from 'node:fs';
+import { homedir } from 'node:os';
+import { join, resolve } from 'node:path';
+import { VERSION } from './version.js';
+/** A registration of this server: by name, by the `clast-ai` binary, or by a path to its cli.js. */
+function isClast(_name, entry) {
+    if (!entry || typeof entry !== 'object')
+        return false;
+    const command = String(entry.command ?? '');
+    const args = Array.isArray(entry.args) ? entry.args.map(String) : [];
+    if (/(^|[\\/])clast-ai(\.cmd|\.exe)?$/i.test(command))
+        return true;
+    // dist/cli.js, and dist/server/index.js as the 0.1 README registered a build from source.
+    if (args.some(a => /clast[^\\/]*[\\/]dist[\\/](cli|server[\\/]index)\.js$/i.test(a)))
+        return true;
+    // `npx clast-ai`, `npx -y clast-ai@0.1`
+    if (/(^|[\\/])npx(\.cmd)?$/i.test(command) && args.some(a => /^clast-ai(@|$)/.test(a)))
+        return true;
+    return false;
+}
+function readJson(path) {
+    try {
+        return JSON.parse(readFileSync(path, 'utf8'));
+    }
+    catch {
+        return null;
+    }
+}
+function describe(entry) {
+    return [entry.command ?? '', ...(Array.isArray(entry.args) ? entry.args.map(String) : [])].join(' ').trim();
+}
+/** Is the clast plugin installed for this user? */
+/**
+ * Where Claude Code keeps its configuration: `~/.claude.json` and `~/.claude/`, or both inside
+ * CLAUDE_CONFIG_DIR when that is set.
+ */
+function claudePaths(home) {
+    const dir = process.env.CLAUDE_CONFIG_DIR;
+    return dir
+        ? { config: join(dir, '.claude.json'), plugins: join(dir, 'plugins') }
+        : { config: join(home, '.claude.json'), plugins: join(home, '.claude', 'plugins') };
+}
+export function pluginInstalled(home) {
+    const installed = readJson(join(claudePaths(home).plugins, 'installed_plugins.json'));
+    const plugins = (installed?.plugins ?? {});
+    return Object.keys(plugins).some(id => /^clast@/.test(id));
+}
+/** Everything an older install left behind, without changing anything. */
+export function planMigration(home, cwd) {
+    const actions = [];
+    const config = readJson(claudePaths(home).config);
+    const servers = (config?.mcpServers ?? {});
+    for (const [name, entry] of Object.entries(servers)) {
+        if (isClast(name, entry))
+            actions.push({ kind: 'mcp', scope: 'user', name, dir: cwd, command: describe(entry) });
+    }
+    const projects = (config?.projects ?? {});
+    for (const [dir, project] of Object.entries(projects)) {
+        for (const [name, entry] of Object.entries(project?.mcpServers ?? {})) {
+            if (isClast(name, entry))
+                actions.push({ kind: 'mcp', scope: 'local', name, dir, command: describe(entry) });
+        }
+    }
+    // Written by the old VS Code extension.
+    const settingsFile = join(cwd, '.claude', 'settings.local.json');
+    const settings = readJson(settingsFile);
+    for (const [name, entry] of Object.entries((settings?.mcpServers ?? {}))) {
+        if (isClast(name, entry))
+            actions.push({ kind: 'settings', file: settingsFile, name });
+    }
+    // The v0.1 index. v0.2 keeps its own file (.clast/index.db) and never reads this one.
+    const old = ['clast.db', 'clast.db-wal', 'clast.db-shm'].map(f => join(cwd, '.clast', f)).filter(f => existsSync(f));
+    if (old.length)
+        actions.push({ kind: 'index', files: old });
+    // A team's shared file is theirs to change.
+    const sharedFile = join(cwd, '.mcp.json');
+    const shared = readJson(sharedFile);
+    for (const [name, entry] of Object.entries((shared?.mcpServers ?? {}))) {
+        if (isClast(name, entry))
+            actions.push({ kind: 'shared', file: sharedFile, name });
+    }
+    return actions;
+}
+function claudeRemove(name, scope, cwd) {
+    const windows = process.platform === 'win32';
+    // Fixed words plus a server name restricted to safe characters: nothing to escape.
+    if (!/^[\w.-]+$/.test(name))
+        return false;
+    const result = windows
+        ? spawnSync(`claude mcp remove ${name} -s ${scope}`, { cwd, shell: true, stdio: 'ignore', windowsHide: true, timeout: 30_000 })
+        : spawnSync('claude', ['mcp', 'remove', name, '-s', scope], { cwd, stdio: 'ignore', timeout: 30_000 });
+    return result.status === 0;
+}
+function line(a) {
+    switch (a.kind) {
+        case 'mcp':
+            return a.scope === 'user'
+                ? `server "${a.name}" registered for all projects (${a.command})`
+                : `server "${a.name}" registered for ${a.dir} (${a.command})`;
+        case 'settings':
+            return `server "${a.name}" in ${a.file} (written by the old VS Code extension)`;
+        case 'index':
+            return `v0.1 index: ${a.files.join(', ')}`;
+        case 'shared':
+            return `server "${a.name}" in ${a.file} (shared with your team: not changed; remove it there if everyone uses the plugin)`;
+    }
+}
+export async function migrate(opts = {}) {
+    const home = opts.home ?? homedir();
+    const cwd = resolve(opts.cwd ?? process.env.CLAST_PROJECT_DIR ?? process.env.CLAUDE_PROJECT_DIR ?? process.cwd());
+    const stateDir = process.env.CLAUDE_PLUGIN_DATA || join(home, '.clast-ai');
+    const marker = join(stateDir, 'migrated.json');
+    const plugin = pluginInstalled(home);
+    if (opts.auto) {
+        // Only the plugin starts this, but be sure: without it the registrations are the only install there is.
+        if (!plugin)
+            return '';
+        const done = readJson(marker);
+        const fresh = done?.version !== VERSION;
+        // The registrations are checked once per version; a project's old index whenever it is seen.
+        const plan = planMigration(home, cwd).filter(a => a.kind === 'index' || (fresh && a.kind !== 'shared'));
+        const report = plan.length ? apply(plan, opts) : [];
+        try {
+            mkdirSync(stateDir, { recursive: true });
+            if (fresh)
+                writeFileSync(marker, JSON.stringify({ version: VERSION, at: new Date().toISOString() }) + '\n');
+            if (report.length) {
+                appendFileSync(join(stateDir, 'migrate.log'), `${new Date().toISOString()} clast ${VERSION}\n${report.map(r => '  ' + r).join('\n')}\n`);
+            }
+        }
+        catch {
+            // A read-only home directory must not stop the server.
+        }
+        return report.join('\n');
+    }
+    const plan = planMigration(home, cwd);
+    const out = [];
+    const removable = plan.filter(a => a.kind !== 'shared');
+    const blocked = !plugin && !opts.force;
+    if (plan.length === 0) {
+        out.push('nothing to migrate: no older clast registration or index found.');
+    }
+    else if (!opts.apply) {
+        out.push(`found ${plan.length} leftover${plan.length === 1 ? '' : 's'} of an older clast install:`);
+        for (const a of plan)
+            out.push(`  - ${line(a)}`);
+        if (removable.length) {
+            out.push(blocked
+                ? 'The clast plugin is not installed, so the registrations above are your only install. Install the plugin ' +
+                    '(/plugin marketplace add xls/clast, /plugin install clast@clast) and run this again, or pass --force.'
+                : 'Run `clast-ai migrate --apply` to remove them (the plugin provides the server).');
+        }
+    }
+    else {
+        const todo = blocked ? removable.filter(a => a.kind === 'index') : removable;
+        out.push(...apply(todo, opts));
+        for (const a of plan.filter(p => p.kind === 'shared'))
+            out.push(`left alone: ${line(a)}`);
+        if (blocked && removable.some(a => a.kind !== 'index')) {
+            out.push('registrations kept: the clast plugin is not installed (pass --force to remove them anyway).');
+        }
+        if (todo.some(a => a.kind === 'mcp' || a.kind === 'settings'))
+            out.push('Restart Claude Code to apply.');
+    }
+    if (!plugin)
+        out.push('plugin: not installed.');
+    return out.join('\n');
+}
+function apply(plan, opts) {
+    const remove = opts.remove ?? claudeRemove;
+    const report = [];
+    for (const a of plan) {
+        try {
+            if (a.kind === 'mcp') {
+                if (a.scope === 'local' && !existsSync(a.dir)) {
+                    report.push(`skipped (directory no longer exists): ${line(a)}`);
+                    continue;
+                }
+                report.push(`${remove(a.name, a.scope, a.dir) ? 'removed' : 'could not remove (is the claude CLI on PATH?)'}: ${line(a)}`);
+            }
+            else if (a.kind === 'settings') {
+                const settings = readJson(a.file);
+                const servers = settings?.mcpServers;
+                if (settings && servers && a.name in servers) {
+                    delete servers[a.name];
+                    if (Object.keys(servers).length === 0)
+                        delete settings.mcpServers;
+                    writeFileSync(a.file, JSON.stringify(settings, null, 2) + '\n');
+                    report.push(`removed: ${line(a)}`);
+                }
+            }
+            else if (a.kind === 'index') {
+                for (const f of a.files)
+                    rmSync(f, { force: true });
+                report.push(`deleted: ${line(a)}`);
+            }
+        }
+        catch (err) {
+            report.push(`failed: ${line(a)}: ${err instanceof Error ? err.message : err}`);
+        }
+    }
+    return report;
+}
+//# sourceMappingURL=migrate.js.map

package/dist/migrate.js.map

@@ -0,0 +1 @@
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package/dist/version.d.ts

@@ -1,2 +1,2 @@
 /** Package version (keep in sync with package.json; checked by a test). */
-export declare const VERSION = "0.2.0";
+export declare const VERSION = "0.2.2";

package/dist/version.js

@@ -1,3 +1,3 @@
 /** Package version (keep in sync with package.json; checked by a test). */
-export const VERSION = '0.2.0';
+export const VERSION = '0.2.2';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "clast-ai",
-  "version": "0.2.0",
+  "version": "0.2.2",
   "description": "Code index MCP server for LLM coding agents: ranked symbol search, exact symbol source, type-aware call graph, references, type hierarchy and git change impact",
   "main": "dist/engine.js",
   "bin": {

package/plugin/server.mjs

@@ -2,17 +2,26 @@
 // Starts the clast MCP server for the Claude Code plugin. A plugin is installed by cloning the
 // repository, which has no build output, so the server is taken from the first place that has one:
 //   1. this checkout, when it has been built (a development clone),
-//   2. a global `clast-ai` of the same major.minor version,
-//   3. `npx clast-ai@<major.minor>` (downloaded on first use, cached afterwards).
+//   2. a global `clast-ai` of the same minor version that is at least as new as the plugin,
+//   3. `npx clast-ai@<plugin version>` (downloaded on first use, cached afterwards).
 // Standard input and output are passed straight through: they carry the MCP protocol.
+//
+// After the server is up it also runs `clast-ai migrate --apply --auto` in the background. That
+// removes, once per version, what an older install left behind (hand-made MCP registrations that
+// would list every tool twice, the v0.1 index file), so installing or upgrading the plugin is
+// all a user has to do.
 import { spawn, spawnSync } from 'node:child_process';
 import { existsSync, readFileSync } from 'node:fs';
+import { tmpdir } from 'node:os';
 import { dirname, join } from 'node:path';
 import { fileURLToPath } from 'node:url';
 
 const root = join(dirname(fileURLToPath(import.meta.url)), '..');
-const wanted = JSON.parse(readFileSync(join(root, 'package.json'), 'utf8')).version.split('.').slice(0, 2).join('.');
+const version = JSON.parse(readFileSync(join(root, 'package.json'), 'utf8')).version;
+const [major, minor, patch] = version.split('.').map(Number);
 const windows = process.platform === 'win32';
+// The project the server indexes: the same order the server itself uses.
+const projectDir = process.env.CLAST_PROJECT_DIR ?? process.env.CLAUDE_PROJECT_DIR ?? process.cwd();
 const log = msg => process.stderr.write(`[clast plugin] ${msg}\n`);
 
 function pick() {
@@ -24,27 +33,46 @@ function pick() {
     ? spawnSync('clast-ai --version', { encoding: 'utf8', shell: true, windowsHide: true })
     : spawnSync('clast-ai', ['--version'], { encoding: 'utf8', windowsHide: true });
   const found = probe.status === 0 ? probe.stdout.trim() : '';
-  if (found.startsWith(wanted + '.')) {
+  const [fMajor, fMinor, fPatch] = found.split('.').map(Number);
+  if (found && fMajor === major && fMinor === minor && fPatch >= patch) {
     return { command: 'clast-ai', args: [], shell: windows, what: `global clast-ai ${found}` };
   }
-  if (found) log(`global clast-ai is ${found}, the plugin needs ${wanted}.x: using npx instead`);
-  return { command: 'npx', args: ['-y', `clast-ai@${wanted}`], shell: windows, what: `npx clast-ai@${wanted}` };
+  if (found) log(`global clast-ai is ${found}, the plugin is ${version}: using npx instead (npm install -g clast-ai updates it)`);
+  // npx runs from a neutral directory: inside a folder whose package.json is itself called clast-ai it
+  // would take that folder for the package and start whatever `clast-ai` is on PATH.
+  return { command: 'npx', args: ['-y', `clast-ai@${version}`], shell: windows, what: `npx clast-ai@${version}`, cwd: tmpdir() };
 }
 
-const major = Number(process.versions.node.split('.')[0]);
-if (major < 22) {
+/** Run the chosen clast-ai with extra arguments. Through a shell (.cmd shims on Windows) the command is one string of fixed words. */
+function run(choice, extra, options) {
+  const args = [...choice.args, ...extra];
+  if (choice.cwd) options = { ...options, cwd: choice.cwd, env: { ...process.env, CLAST_PROJECT_DIR: projectDir } };
+  return choice.shell
+    ? spawn([choice.command, ...args].join(' '), { ...options, shell: true, windowsHide: true })
+    : spawn(choice.command, args, { ...options, windowsHide: true });
+}
+
+if (Number(process.versions.node.split('.')[0]) < 22) {
   log(`Node.js 22.22 or newer is required (this is ${process.versions.node}).`);
   process.exit(1);
 }
 const choice = pick();
 log(`starting ${choice.what}`);
-// Through a shell (needed for .cmd shims on Windows) the command goes in as one string of fixed words.
-const child = choice.shell
-  ? spawn([choice.command, ...choice.args].join(' '), { stdio: 'inherit', shell: true, windowsHide: true })
-  : spawn(choice.command, choice.args, { stdio: 'inherit', windowsHide: true });
+const child = run(choice, [], { stdio: 'inherit' });
 child.on('error', err => {
   log(`could not start the server: ${err.message}. Install it with: npm install -g clast-ai`);
   process.exit(1);
 });
 child.on('exit', (code, signal) => process.exit(code ?? (signal ? 1 : 0)));
 for (const sig of ['SIGINT', 'SIGTERM']) process.on(sig, () => child.kill(sig));
+
+// Clean up after older installs, without holding up or disturbing the server (no shared stdio).
+if (process.env.CLAST_NO_MIGRATE !== '1') {
+  try {
+    const cleanup = run(choice, ['migrate', '--apply', '--auto'], { stdio: 'ignore', detached: !windows });
+    cleanup.on('error', () => {});
+    cleanup.unref();
+  } catch {
+    // Never let the cleanup stop the server.
+  }
+}

package/src/cli.ts

@@ -35,6 +35,8 @@ usage: clast-ai [command] [args] [--root <dir>]
   unused [path]              dead code   [--kind k] [--lang l] [--limit n] [--no-exported]
   stats [what] [name]        exact counts: inventory | symbols | subtypes | calls | text | imports | endpoints | database
                              [--kind k] [--on receiver] [--path p] [--lang l] [--group-by g] [--depth n] [--limit n] [--tests]
+  migrate [--apply]          find (and with --apply remove) what older installs left behind: duplicate
+                             MCP registrations next to the plugin, the v0.1 index file
   parse <file> [--json]      debug: show what the extractor produces for a file
   ast <file>                 debug: dump the tree-sitter syntax tree
 
@@ -63,7 +65,7 @@ interface Parsed {
 }
 
 const BOOLEAN_FLAGS = new Set([
-  'force', 'json', 'regex', 'no-body', 'no-scan', 'no-tests', 'tests', 'uncertain', 'help', 'version', 'all', 'no-exported',
+  'force', 'json', 'regex', 'no-body', 'no-scan', 'no-tests', 'tests', 'uncertain', 'help', 'version', 'all', 'no-exported', 'apply', 'auto',
 ]);
 
 function parseArgs(argv: string[]): Parsed {
@@ -105,6 +107,13 @@ async function main(): Promise<void> {
     return;
   }
 
+  if (cmd === 'migrate') {
+    const { migrate } = await import('./migrate.js');
+    const out = await migrate({ apply: flags.has('apply'), auto: flags.has('auto'), force: flags.has('force'), cwd: str('root') });
+    if (out) console.log(out);
+    return;
+  }
+
   if (cmd === 'parse' || cmd === 'ast') {
     const file = positional[0];
     if (!file) throw new Error(`usage: clast-ai ${cmd} <file>`);

package/src/migrate.ts

@@ -0,0 +1,225 @@
+import { spawnSync } from 'node:child_process';
+import { appendFileSync, existsSync, mkdirSync, readFileSync, rmSync, writeFileSync } from 'node:fs';
+import { homedir } from 'node:os';
+import { join, resolve } from 'node:path';
+import { VERSION } from './version.js';
+
+// ---------------------------------------------------------------------------
+// clast-ai migrate: remove what older installs left behind
+// ---------------------------------------------------------------------------
+//
+// Before the plugin, clast was registered by hand (`claude mcp add`) or by the old VS Code extension
+// (`.claude/settings.local.json`). With the plugin installed those registrations start a second copy
+// of the server and list every tool twice. This finds them, and the v0.1 index file, and removes them.
+
+export interface MigrateOptions {
+  /** Make the changes. Default: only report. */
+  apply?: boolean;
+  /** Run from the plugin at session start: once per version, silent, only when the plugin is installed. */
+  auto?: boolean;
+  /** Remove hand-made registrations even when the plugin is not installed. */
+  force?: boolean;
+  home?: string;
+  cwd?: string;
+  /** Replaces `claude mcp remove` (tests). Returns true on success. */
+  remove?: (name: string, scope: 'user' | 'local', cwd: string) => boolean;
+}
+
+export type Action =
+  | { kind: 'mcp'; scope: 'user' | 'local'; name: string; dir: string; command: string }
+  | { kind: 'settings'; file: string; name: string }
+  | { kind: 'index'; files: string[] }
+  | { kind: 'shared'; file: string; name: string };
+
+interface ServerEntry {
+  command?: string;
+  args?: unknown[];
+}
+
+/** A registration of this server: by name, by the `clast-ai` binary, or by a path to its cli.js. */
+function isClast(_name: string, entry: ServerEntry | undefined): boolean {
+  if (!entry || typeof entry !== 'object') return false;
+  const command = String(entry.command ?? '');
+  const args = Array.isArray(entry.args) ? entry.args.map(String) : [];
+  if (/(^|[\\/])clast-ai(\.cmd|\.exe)?$/i.test(command)) return true;
+  // dist/cli.js, and dist/server/index.js as the 0.1 README registered a build from source.
+  if (args.some(a => /clast[^\\/]*[\\/]dist[\\/](cli|server[\\/]index)\.js$/i.test(a))) return true;
+  // `npx clast-ai`, `npx -y clast-ai@0.1`
+  if (/(^|[\\/])npx(\.cmd)?$/i.test(command) && args.some(a => /^clast-ai(@|$)/.test(a))) return true;
+  return false;
+}
+
+function readJson(path: string): Record<string, unknown> | null {
+  try {
+    return JSON.parse(readFileSync(path, 'utf8')) as Record<string, unknown>;
+  } catch {
+    return null;
+  }
+}
+
+function describe(entry: ServerEntry): string {
+  return [entry.command ?? '', ...(Array.isArray(entry.args) ? entry.args.map(String) : [])].join(' ').trim();
+}
+
+/** Is the clast plugin installed for this user? */
+/**
+ * Where Claude Code keeps its configuration: `~/.claude.json` and `~/.claude/`, or both inside
+ * CLAUDE_CONFIG_DIR when that is set.
+ */
+function claudePaths(home: string): { config: string; plugins: string } {
+  const dir = process.env.CLAUDE_CONFIG_DIR;
+  return dir
+    ? { config: join(dir, '.claude.json'), plugins: join(dir, 'plugins') }
+    : { config: join(home, '.claude.json'), plugins: join(home, '.claude', 'plugins') };
+}
+
+export function pluginInstalled(home: string): boolean {
+  const installed = readJson(join(claudePaths(home).plugins, 'installed_plugins.json'));
+  const plugins = (installed?.plugins ?? {}) as Record<string, unknown>;
+  return Object.keys(plugins).some(id => /^clast@/.test(id));
+}
+
+/** Everything an older install left behind, without changing anything. */
+export function planMigration(home: string, cwd: string): Action[] {
+  const actions: Action[] = [];
+  const config = readJson(claudePaths(home).config);
+  const servers = (config?.mcpServers ?? {}) as Record<string, ServerEntry>;
+  for (const [name, entry] of Object.entries(servers)) {
+    if (isClast(name, entry)) actions.push({ kind: 'mcp', scope: 'user', name, dir: cwd, command: describe(entry) });
+  }
+  const projects = (config?.projects ?? {}) as Record<string, { mcpServers?: Record<string, ServerEntry> }>;
+  for (const [dir, project] of Object.entries(projects)) {
+    for (const [name, entry] of Object.entries(project?.mcpServers ?? {})) {
+      if (isClast(name, entry)) actions.push({ kind: 'mcp', scope: 'local', name, dir, command: describe(entry) });
+    }
+  }
+  // Written by the old VS Code extension.
+  const settingsFile = join(cwd, '.claude', 'settings.local.json');
+  const settings = readJson(settingsFile);
+  for (const [name, entry] of Object.entries((settings?.mcpServers ?? {}) as Record<string, ServerEntry>)) {
+    if (isClast(name, entry)) actions.push({ kind: 'settings', file: settingsFile, name });
+  }
+  // The v0.1 index. v0.2 keeps its own file (.clast/index.db) and never reads this one.
+  const old = ['clast.db', 'clast.db-wal', 'clast.db-shm'].map(f => join(cwd, '.clast', f)).filter(f => existsSync(f));
+  if (old.length) actions.push({ kind: 'index', files: old });
+  // A team's shared file is theirs to change.
+  const sharedFile = join(cwd, '.mcp.json');
+  const shared = readJson(sharedFile);
+  for (const [name, entry] of Object.entries((shared?.mcpServers ?? {}) as Record<string, ServerEntry>)) {
+    if (isClast(name, entry)) actions.push({ kind: 'shared', file: sharedFile, name });
+  }
+  return actions;
+}
+
+function claudeRemove(name: string, scope: 'user' | 'local', cwd: string): boolean {
+  const windows = process.platform === 'win32';
+  // Fixed words plus a server name restricted to safe characters: nothing to escape.
+  if (!/^[\w.-]+$/.test(name)) return false;
+  const result = windows
+    ? spawnSync(`claude mcp remove ${name} -s ${scope}`, { cwd, shell: true, stdio: 'ignore', windowsHide: true, timeout: 30_000 })
+    : spawnSync('claude', ['mcp', 'remove', name, '-s', scope], { cwd, stdio: 'ignore', timeout: 30_000 });
+  return result.status === 0;
+}
+
+function line(a: Action): string {
+  switch (a.kind) {
+    case 'mcp':
+      return a.scope === 'user'
+        ? `server "${a.name}" registered for all projects (${a.command})`
+        : `server "${a.name}" registered for ${a.dir} (${a.command})`;
+    case 'settings':
+      return `server "${a.name}" in ${a.file} (written by the old VS Code extension)`;
+    case 'index':
+      return `v0.1 index: ${a.files.join(', ')}`;
+    case 'shared':
+      return `server "${a.name}" in ${a.file} (shared with your team: not changed; remove it there if everyone uses the plugin)`;
+  }
+}
+
+export async function migrate(opts: MigrateOptions = {}): Promise<string> {
+  const home = opts.home ?? homedir();
+  const cwd = resolve(opts.cwd ?? process.env.CLAST_PROJECT_DIR ?? process.env.CLAUDE_PROJECT_DIR ?? process.cwd());
+  const stateDir = process.env.CLAUDE_PLUGIN_DATA || join(home, '.clast-ai');
+  const marker = join(stateDir, 'migrated.json');
+  const plugin = pluginInstalled(home);
+
+  if (opts.auto) {
+    // Only the plugin starts this, but be sure: without it the registrations are the only install there is.
+    if (!plugin) return '';
+    const done = readJson(marker);
+    const fresh = done?.version !== VERSION;
+    // The registrations are checked once per version; a project's old index whenever it is seen.
+    const plan = planMigration(home, cwd).filter(a => a.kind === 'index' || (fresh && a.kind !== 'shared'));
+    const report = plan.length ? apply(plan, opts) : [];
+    try {
+      mkdirSync(stateDir, { recursive: true });
+      if (fresh) writeFileSync(marker, JSON.stringify({ version: VERSION, at: new Date().toISOString() }) + '\n');
+      if (report.length) {
+        appendFileSync(join(stateDir, 'migrate.log'), `${new Date().toISOString()} clast ${VERSION}\n${report.map(r => '  ' + r).join('\n')}\n`);
+      }
+    } catch {
+      // A read-only home directory must not stop the server.
+    }
+    return report.join('\n');
+  }
+
+  const plan = planMigration(home, cwd);
+  const out: string[] = [];
+  const removable = plan.filter(a => a.kind !== 'shared');
+  const blocked = !plugin && !opts.force;
+  if (plan.length === 0) {
+    out.push('nothing to migrate: no older clast registration or index found.');
+  } else if (!opts.apply) {
+    out.push(`found ${plan.length} leftover${plan.length === 1 ? '' : 's'} of an older clast install:`);
+    for (const a of plan) out.push(`  - ${line(a)}`);
+    if (removable.length) {
+      out.push(
+        blocked
+          ? 'The clast plugin is not installed, so the registrations above are your only install. Install the plugin ' +
+              '(/plugin marketplace add xls/clast, /plugin install clast@clast) and run this again, or pass --force.'
+          : 'Run `clast-ai migrate --apply` to remove them (the plugin provides the server).'
+      );
+    }
+  } else {
+    const todo = blocked ? removable.filter(a => a.kind === 'index') : removable;
+    out.push(...apply(todo, opts));
+    for (const a of plan.filter(p => p.kind === 'shared')) out.push(`left alone: ${line(a)}`);
+    if (blocked && removable.some(a => a.kind !== 'index')) {
+      out.push('registrations kept: the clast plugin is not installed (pass --force to remove them anyway).');
+    }
+    if (todo.some(a => a.kind === 'mcp' || a.kind === 'settings')) out.push('Restart Claude Code to apply.');
+  }
+  if (!plugin) out.push('plugin: not installed.');
+  return out.join('\n');
+}
+
+function apply(plan: Action[], opts: MigrateOptions): string[] {
+  const remove = opts.remove ?? claudeRemove;
+  const report: string[] = [];
+  for (const a of plan) {
+    try {
+      if (a.kind === 'mcp') {
+        if (a.scope === 'local' && !existsSync(a.dir)) {
+          report.push(`skipped (directory no longer exists): ${line(a)}`);
+          continue;
+        }
+        report.push(`${remove(a.name, a.scope, a.dir) ? 'removed' : 'could not remove (is the claude CLI on PATH?)'}: ${line(a)}`);
+      } else if (a.kind === 'settings') {
+        const settings = readJson(a.file);
+        const servers = settings?.mcpServers as Record<string, unknown> | undefined;
+        if (settings && servers && a.name in servers) {
+          delete servers[a.name];
+          if (Object.keys(servers).length === 0) delete settings.mcpServers;
+          writeFileSync(a.file, JSON.stringify(settings, null, 2) + '\n');
+          report.push(`removed: ${line(a)}`);
+        }
+      } else if (a.kind === 'index') {
+        for (const f of a.files) rmSync(f, { force: true });
+        report.push(`deleted: ${line(a)}`);
+      }
+    } catch (err) {
+      report.push(`failed: ${line(a)}: ${err instanceof Error ? err.message : err}`);
+    }
+  }
+  return report;
+}

package/src/version.ts

@@ -1,2 +1,2 @@
 /** Package version (keep in sync with package.json; checked by a test). */
-export const VERSION = '0.2.0';
+export const VERSION = '0.2.2';

package/tsconfig.json

@@ -20,4 +20,4 @@
   },
   "include": ["src/**/*.ts"],
   "exclude": ["node_modules", "dist", "test"]
-}
+}