@neurodock/cli 0.1.0

package/CHANGELOG.md

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+# @neurodock/cli changelog
+
+## 0.1.0 (unreleased)
+
+First implementation. Phase 1 deliverable per .
+
+- `neurodock init` — detect Claude Desktop, Claude Code, and Cursor on macOS, Linux, and Windows; install profile from `profile.example.yaml` (default) or `profile.minimal.yaml`; wire three Python MCP servers into the detected client configs.
+- `neurodock doctor` — checklist diagnostic: Node >= 22, `uv` available, Python available, profile presence + schema validity, client config JSON syntax, NeuroDock server wiring.
+- `neurodock profile validate` — Ajv-driven schema validation with field-path violation output.
+- `neurodock profile show` — print the resolved profile with loader defaults applied (per ADR 0004 §15).
+- `--dry-run` and `--yes` flags on `init`.
+- Preserves existing `mcpServers` keys, comments in profile YAML, and unknown top-level keys (forward-compat per ADR 0004).
+- 24+ unit tests across paths, validator, defaults, client adapters, init, and doctor.

package/LICENSE

@@ -0,0 +1,11 @@
+NeuroDock is licensed under the GNU Affero General Public License v3.0 or later.
+
+SPDX-License-Identifier: AGPL-3.0-or-later
+
+The canonical license text is available at:
+https://www.gnu.org/licenses/agpl-3.0.txt
+
+A local copy can be added by running:
+  curl -o LICENSE-AGPL-3.0 https://www.gnu.org/licenses/agpl-3.0.txt
+
+License intent confirmed by the founding council at first meeting (see GOVERNANCE.md).

package/README.md

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+# @neurodock/cli
+
+The `neurodock` installer and diagnostic CLI.
+
+Status: Phase 1 (v0.1 developer preview).
+
+## Quickstart
+
+```bash
+# From a published package once it lands on npm:
+npx neurodock init
+
+# From a fresh clone of the monorepo:
+pnpm install
+pnpm --filter @neurodock/cli build
+node packages/cli/dist/index.js init
+```
+
+`neurodock init` wires three Python MCP servers (chronometric, cognitive-graph,
+task-fractionator) into every MCP-aware client it can detect.
+
+**Prerequisite:** the CLI does not install Python deps for you. From a clone
+run `uv sync` (or `pip install -e packages/mcp-chronometric` etc.) so the
+`neurodock-mcp-*` console entry points are on `$PATH` for `uv run`. From a
+published install this matures into `uv tool install neurodock-mcp-*`.
+
+## Commands
+
+| Command | What it does |
+|---|---|
+| `neurodock init` | Install MCP servers into Claude Desktop / Claude Code / Cursor. |
+| `neurodock doctor` | Diagnose your install — profile validity, client wiring, tool availability. |
+| `neurodock profile validate` | Validate `~/.neurodock/profile.yaml` against the v0.1 schema. |
+| `neurodock profile show` | Print the resolved profile with loader defaults applied. |
+
+### `neurodock init`
+
+```
+neurodock init [--client=claude-desktop|claude-code|cursor|all] \
+               [--profile=minimal|example] \
+               [--dry-run] [--yes]
+```
+
+- `--client` defaults to `all`. With `all` we only act on already-existing client configs.
+- `--profile` defaults to `example` (the worked "T" profile). Use `minimal` for the shortest valid file.
+- `--dry-run` prints the diff and exits 0.
+- `--yes` overwrites colliding `mcpServers` keys without prompting.
+
+What `init` does, in order:
+
+1. Detects supported clients per platform (see "Detection locations" below).
+2. Copies `profile.example.yaml` or `profile.minimal.yaml` to `~/.neurodock/profile.yaml` if it does not already exist. Sets `identity.display_name` from `$USER` / `%USERNAME%`.
+3. Adds three `mcpServers` entries (`neurodock-chronometric`, `neurodock-cognitive-graph`, `neurodock-task-fractionator`) to each detected client's config.
+4. Preserves all unrelated keys, comments, and unknown server entries already in those configs.
+
+Idempotent. Re-running with no changes is a no-op. Collisions on a previous
+key are skipped unless `--yes` is supplied.
+
+### Detection locations
+
+| Client | Platform | Path |
+|---|---|---|
+| Claude Desktop | macOS | `~/Library/Application Support/Claude/claude_desktop_config.json` |
+| Claude Desktop | Windows | `%APPDATA%\Claude\claude_desktop_config.json` |
+| Claude Desktop | Linux | `~/.config/Claude/claude_desktop_config.json` |
+| Claude Code | All | `./.claude/settings.json` (project, preferred) then `~/.claude/settings.json` (user) |
+| Cursor | All | `./.cursor/mcp.json` (project, preferred) then `~/.cursor/mcp.json` (user) |
+
+### Profile precedence
+
+Loader precedence (highest first):
+
+1. `$NEURODOCK_PROFILE_PATH`
+2. `$XDG_CONFIG_HOME/neurodock/profile.yaml`
+3. `~/.neurodock/profile.yaml`
+
+## Build and test
+
+```bash
+cd packages/cli
+pnpm install
+pnpm run typecheck
+pnpm run test
+pnpm run build
+node dist/index.js --version
+node dist/index.js --help
+```
+
+## Design notes
+
+- Strict TypeScript, NodeNext modules, ES2022 target.
+- Profile YAML round-trip preserves comments (the `yaml` package's
+  `parseDocument` API), per ADR 0004 §14.
+- All loader defaults live in `src/profile/defaults.ts` and mirror
+  `profile.schema.json` — JSON Schema validation does not apply defaults
+  itself, so the loader does.
+- No telemetry, no remote calls, no auto-install of Python packages.
+
+## License
+
+AGPL-3.0-or-later.

package/dist/clients/claude-code.d.ts

@@ -0,0 +1,3 @@
+import type { ClientAdapter } from "./index.js";
+export declare const claudeCodeAdapter: ClientAdapter;
+//# sourceMappingURL=claude-code.d.ts.map

package/dist/clients/claude-code.d.ts.map

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package/dist/clients/claude-code.js

@@ -0,0 +1,22 @@
+import { claudeCodeConfigPaths } from "../lib/paths.js";
+export const claudeCodeAdapter = {
+    id: "claude-code",
+    displayName: "Claude Code",
+    configPaths(env) {
+        const paths = claudeCodeConfigPaths(env);
+        return [
+            { path: paths.project, scope: "project" },
+            { path: paths.user, scope: "user" },
+        ];
+    },
+    shapeConfig(existing, mcpServers) {
+        const base = isObject(existing) ? { ...existing } : {};
+        const prev = isObject(base["mcpServers"]) ? base["mcpServers"] : {};
+        base["mcpServers"] = { ...prev, ...mcpServers };
+        return base;
+    },
+};
+function isObject(x) {
+    return typeof x === "object" && x !== null && !Array.isArray(x);
+}
+//# sourceMappingURL=claude-code.js.map

package/dist/clients/claude-code.js.map

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package/dist/clients/claude-desktop.d.ts

@@ -0,0 +1,3 @@
+import type { ClientAdapter } from "./index.js";
+export declare const claudeDesktopAdapter: ClientAdapter;
+//# sourceMappingURL=claude-desktop.d.ts.map

package/dist/clients/claude-desktop.d.ts.map

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package/dist/clients/claude-desktop.js

@@ -0,0 +1,18 @@
+import { claudeDesktopConfigPath } from "../lib/paths.js";
+export const claudeDesktopAdapter = {
+    id: "claude-desktop",
+    displayName: "Claude Desktop",
+    configPaths(env) {
+        return [{ path: claudeDesktopConfigPath(env), scope: "user" }];
+    },
+    shapeConfig(existing, mcpServers) {
+        const base = isObject(existing) ? { ...existing } : {};
+        const prev = isObject(base["mcpServers"]) ? base["mcpServers"] : {};
+        base["mcpServers"] = { ...prev, ...mcpServers };
+        return base;
+    },
+};
+function isObject(x) {
+    return typeof x === "object" && x !== null && !Array.isArray(x);
+}
+//# sourceMappingURL=claude-desktop.js.map

package/dist/clients/claude-desktop.js.map

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package/dist/clients/cursor.d.ts

@@ -0,0 +1,3 @@
+import type { ClientAdapter } from "./index.js";
+export declare const cursorAdapter: ClientAdapter;
+//# sourceMappingURL=cursor.d.ts.map

package/dist/clients/cursor.d.ts.map

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package/dist/clients/cursor.js

@@ -0,0 +1,22 @@
+import { cursorConfigPaths } from "../lib/paths.js";
+export const cursorAdapter = {
+    id: "cursor",
+    displayName: "Cursor",
+    configPaths(env) {
+        const paths = cursorConfigPaths(env);
+        return [
+            { path: paths.project, scope: "project" },
+            { path: paths.user, scope: "user" },
+        ];
+    },
+    shapeConfig(existing, mcpServers) {
+        const base = isObject(existing) ? { ...existing } : {};
+        const prev = isObject(base["mcpServers"]) ? base["mcpServers"] : {};
+        base["mcpServers"] = { ...prev, ...mcpServers };
+        return base;
+    },
+};
+function isObject(x) {
+    return typeof x === "object" && x !== null && !Array.isArray(x);
+}
+//# sourceMappingURL=cursor.js.map

package/dist/clients/cursor.js.map

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package/dist/clients/index.d.ts

@@ -0,0 +1,17 @@
+import type { ClientId, McpServerEntry } from "../types.js";
+import type { EnvSnapshot } from "../lib/env.js";
+export interface ClientAdapter {
+    readonly id: ClientId;
+    readonly displayName: string;
+    /** Possible config file locations, highest precedence first. */
+    configPaths(env: EnvSnapshot): ReadonlyArray<ConfigCandidate>;
+    /** Wrap an mcpServers map into the shape this client expects. */
+    shapeConfig(existing: unknown, mcpServers: Record<string, McpServerEntry>): unknown;
+}
+export interface ConfigCandidate {
+    readonly path: string;
+    readonly scope: "user" | "project";
+}
+export declare const allAdapters: ReadonlyArray<ClientAdapter>;
+export declare function adapterFor(id: ClientId): ClientAdapter;
+//# sourceMappingURL=index.d.ts.map

package/dist/clients/index.d.ts.map

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package/dist/clients/index.js

@@ -0,0 +1,16 @@
+import { claudeDesktopAdapter } from "./claude-desktop.js";
+import { claudeCodeAdapter } from "./claude-code.js";
+import { cursorAdapter } from "./cursor.js";
+export const allAdapters = [
+    claudeDesktopAdapter,
+    claudeCodeAdapter,
+    cursorAdapter,
+];
+export function adapterFor(id) {
+    const found = allAdapters.find((a) => a.id === id);
+    if (!found) {
+        throw new Error(`Unknown client id: ${id}`);
+    }
+    return found;
+}
+//# sourceMappingURL=index.js.map

package/dist/clients/index.js.map

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package/dist/commands/doctor.d.ts

@@ -0,0 +1,7 @@
+import type { CheckResult } from "../types.js";
+export interface DoctorResult {
+    readonly checks: ReadonlyArray<CheckResult>;
+    readonly ok: boolean;
+}
+export declare function runDoctor(): Promise<DoctorResult>;
+//# sourceMappingURL=doctor.d.ts.map

package/dist/commands/doctor.d.ts.map

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package/dist/commands/doctor.js

@@ -0,0 +1,107 @@
+import { execFileSync } from "node:child_process";
+import { readFileSync, existsSync } from "node:fs";
+import { readEnv } from "../lib/env.js";
+import { profilePath, detectClients } from "../lib/paths.js";
+import { loadProfileFromFile } from "../profile/loader.js";
+import { validateProfile } from "../profile/validator.js";
+import { parseJsonSafely } from "../lib/json-patch.js";
+export async function runDoctor() {
+    const env = readEnv();
+    const checks = [];
+    checks.push(checkNodeVersion());
+    checks.push(checkCommandAvailable("uv", ["--version"]));
+    checks.push(checkCommandAvailable("python3", ["--version"], "python3 or python >= 3.11"));
+    // Profile presence + validity.
+    const pPath = profilePath(env);
+    if (!existsSync(pPath)) {
+        checks.push({
+            name: "Profile exists",
+            status: "FAIL",
+            detail: `No profile at ${pPath}. Run 'neurodock init' to create one.`,
+        });
+    }
+    else {
+        checks.push({ name: "Profile exists", status: "PASS", detail: pPath });
+        try {
+            const loaded = loadProfileFromFile(pPath);
+            const result = validateProfile(loaded.raw);
+            if (result.valid) {
+                checks.push({ name: "Profile schema valid", status: "PASS" });
+            }
+            else {
+                checks.push({
+                    name: "Profile schema valid",
+                    status: "FAIL",
+                    detail: result.violations.map((v) => `${v.path}: ${v.message}`).join("; "),
+                });
+            }
+        }
+        catch (err) {
+            checks.push({
+                name: "Profile schema valid",
+                status: "FAIL",
+                detail: err instanceof Error ? err.message : String(err),
+            });
+        }
+    }
+    // Client configs syntax check.
+    const detections = detectClients(env);
+    const existing = detections.filter((d) => d.exists);
+    if (existing.length === 0) {
+        checks.push({
+            name: "Client configs",
+            status: "SKIP",
+            detail: "No supported client config found. Skipping wiring check.",
+        });
+    }
+    else {
+        for (const d of existing) {
+            const raw = readFileSync(d.path, "utf8");
+            const parsed = parseJsonSafely(raw);
+            if (!parsed.ok) {
+                checks.push({
+                    name: `Client config syntax: ${d.id} (${d.scope})`,
+                    status: "FAIL",
+                    detail: `${d.path}: ${parsed.error}`,
+                });
+                continue;
+            }
+            checks.push({
+                name: `Client config syntax: ${d.id} (${d.scope})`,
+                status: "PASS",
+                detail: d.path,
+            });
+            const cfg = (parsed.value ?? {});
+            const servers = cfg.mcpServers ?? {};
+            const wired = Object.keys(servers).filter((k) => k.startsWith("neurodock-"));
+            checks.push({
+                name: `NeuroDock servers wired: ${d.id} (${d.scope})`,
+                status: wired.length > 0 ? "PASS" : "FAIL",
+                detail: wired.length > 0 ? wired.join(", ") : "no neurodock-* entries found",
+            });
+        }
+    }
+    const ok = checks.every((c) => c.status !== "FAIL");
+    return { checks, ok };
+}
+function checkNodeVersion() {
+    const v = process.versions.node;
+    const major = Number.parseInt(v.split(".")[0] ?? "0", 10);
+    if (Number.isFinite(major) && major >= 22) {
+        return { name: "Node >= 22", status: "PASS", detail: `node ${v}` };
+    }
+    return { name: "Node >= 22", status: "FAIL", detail: `node ${v}` };
+}
+function checkCommandAvailable(cmd, args, label) {
+    const name = label ?? `${cmd} available`;
+    try {
+        const out = execFileSync(cmd, args, { stdio: ["ignore", "pipe", "pipe"], timeout: 4000 });
+        const text = out.toString().trim().split("\n")[0] ?? "";
+        return { name, status: "PASS", detail: text };
+    }
+    catch (err) {
+        const detail = err instanceof Error ? err.message.split("\n")[0] ?? "unknown error" : String(err);
+        return { name, status: "FAIL", detail };
+    }
+}
+//# sourceMappingURL=doctor.js.map

package/dist/commands/doctor.js.map

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package/dist/commands/init.d.ts

@@ -0,0 +1,13 @@
+import type { InitDiff, InitOptions } from "../types.js";
+import { readEnv } from "../lib/env.js";
+export interface InitRunResult {
+    readonly diff: InitDiff;
+    readonly applied: boolean;
+    readonly messages: ReadonlyArray<string>;
+}
+export interface InitDependencies {
+    /** Override the environment snapshot (for tests). */
+    readonly envOverrides?: Parameters<typeof readEnv>[0];
+}
+export declare function runInit(options: InitOptions, deps?: InitDependencies): Promise<InitRunResult>;
+//# sourceMappingURL=init.d.ts.map

package/dist/commands/init.d.ts.map

@@ -0,0 +1 @@
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package/dist/commands/init.js

@@ -0,0 +1,189 @@
+import { readFileSync, writeFileSync, mkdirSync, existsSync } from "node:fs";
+import { dirname, join, resolve } from "node:path";
+import { fileURLToPath } from "node:url";
+import { readEnv } from "../lib/env.js";
+import { profilePath, detectClients } from "../lib/paths.js";
+import { adapterFor } from "../clients/index.js";
+import { mergeMcpServers, parseJsonSafely } from "../lib/json-patch.js";
+import { writeProfileFromTemplate } from "../profile/loader.js";
+import { buildMcpServers, detectRepoRoot } from "../lib/mcp-entries.js";
+export async function runInit(options, deps = {}) {
+    const env = readEnv(deps.envOverrides ?? {});
+    const messages = [];
+    // 1. Detect clients.
+    const detections = detectClients(env);
+    const targets = pickTargets(detections, options.client);
+    const detectedTargets = targets.filter((t) => t.exists);
+    if (options.client !== "all" && targets.length === 0) {
+        messages.push(`No supported client locations exist for '${options.client}'.`);
+    }
+    if (options.client === "all" && detectedTargets.length === 0) {
+        messages.push("No supported MCP client detected.");
+        messages.push("Looked for:");
+        for (const t of targets) {
+            messages.push(`  - ${t.id} (${t.scope}): ${t.path}`);
+        }
+        messages.push("See: https://docs.neurodock.org/install#supported-clients");
+        return {
+            diff: { profileAction: "skipped", profilePath: profilePath(env), clients: [] },
+            applied: false,
+            messages,
+        };
+    }
+    // 2. Build the desired mcpServers entries once.
+    const repoRoot = detectRepoRoot(env);
+    const desiredServers = buildMcpServers({
+        ...(repoRoot !== undefined ? { repoRoot } : {}),
+    });
+    // 3. Profile.
+    const pPath = profilePath(env);
+    const profileAction = existsSync(pPath) ? "exists" : "create";
+    // 4. Per-client diff.
+    const clientDiffs = [];
+    // For "all" mode, only act on already-existing locations; for explicit
+    // client choice, act on the highest-precedence path even if absent.
+    const actOn = options.client === "all" ? detectedTargets : targets.slice(0, 1);
+    for (const target of actOn) {
+        const diff = await diffClient(target, desiredServers, options);
+        clientDiffs.push(diff);
+    }
+    const diff = {
+        profileAction,
+        profilePath: pPath,
+        clients: clientDiffs,
+    };
+    if (options.dryRun) {
+        return {
+            diff,
+            applied: false,
+            messages: ["Dry run. No changes written.", ...messages, ...formatDiff(diff)],
+        };
+    }
+    // 5. Apply.
+    // 5a. Profile.
+    if (profileAction === "create") {
+        const templatePath = resolveTemplatePath(options.profile);
+        writeProfileFromTemplate({
+            templatePath,
+            targetPath: pPath,
+            displayName: env.user,
+        });
+        messages.push(`Profile created at ${pPath}.`);
+    }
+    else {
+        messages.push(`Profile already exists at ${pPath}. Left untouched.`);
+    }
+    // 5b. Client configs.
+    for (const cd of clientDiffs) {
+        if (cd.action === "create" || cd.action === "update") {
+            applyClientDiff(cd, desiredServers, options.yes);
+            messages.push(`Wired ${cd.client} at ${cd.path}.`);
+        }
+        else if (cd.action === "no-change") {
+            messages.push(`${cd.client} already wired at ${cd.path}.`);
+        }
+        else if (cd.action === "skip") {
+            messages.push(`Skipped ${cd.client} at ${cd.path}: ${cd.reason ?? "collision (re-run with --yes to overwrite)"}.`);
+        }
+    }
+    // 5c. What-next.
+    messages.push("");
+    messages.push("What next:");
+    messages.push("  1. Restart your MCP client so it picks up the new servers.");
+    messages.push(`  2. Edit ${pPath} to set your neurotypes and preferences.`);
+    return { diff, applied: true, messages };
+}
+function pickTargets(detections, client) {
+    if (client === "all")
+        return detections;
+    return detections.filter((d) => d.id === client);
+}
+async function diffClient(target, desired, options) {
+    let existing = null;
+    if (existsSync(target.path)) {
+        const raw = readFileSync(target.path, "utf8");
+        const parsed = parseJsonSafely(raw);
+        if (!parsed.ok) {
+            return {
+                client: target.id,
+                path: target.path,
+                action: "skip",
+                added: [],
+                collisions: [],
+                reason: `existing config is not valid JSON: ${parsed.error}`,
+            };
+        }
+        existing = parsed.value ?? {};
+    }
+    const merge = mergeMcpServers((existing ?? {}), desired, options.yes);
+    if (merge.collisions.length > 0 && !options.yes) {
+        return {
+            client: target.id,
+            path: target.path,
+            action: "skip",
+            added: merge.added,
+            collisions: merge.collisions,
+            reason: "existing keys would be overwritten; re-run with --yes to confirm",
+        };
+    }
+    if (merge.unchanged && existing !== null) {
+        return {
+            client: target.id,
+            path: target.path,
+            action: "no-change",
+            added: [],
+            collisions: [],
+        };
+    }
+    return {
+        client: target.id,
+        path: target.path,
+        action: existing === null ? "create" : "update",
+        added: merge.added,
+        collisions: merge.collisions,
+    };
+}
+function applyClientDiff(cd, desired, overwrite) {
+    const adapter = adapterFor(cd.client);
+    let existing = null;
+    if (existsSync(cd.path)) {
+        const raw = readFileSync(cd.path, "utf8");
+        const parsed = parseJsonSafely(raw);
+        if (parsed.ok)
+            existing = parsed.value;
+    }
+    const merged = mergeMcpServers(existing ?? {}, desired, overwrite);
+    const shaped = adapter.shapeConfig(existing, merged.merged.mcpServers);
+    mkdirSync(dirname(cd.path), { recursive: true });
+    writeFileSync(cd.path, `${JSON.stringify(shaped, null, 2)}\n`, "utf8");
+}
+function resolveTemplatePath(profile) {
+    const filename = profile === "minimal" ? "profile.minimal.yaml" : "profile.example.yaml";
+    const here = dirname(fileURLToPath(import.meta.url));
+    const candidates = [
+        resolve(here, "..", "..", "..", "core", "schemas", filename),
+        resolve(here, "..", "..", "..", "..", "core", "schemas", filename),
+        resolve(here, "..", "..", "core", "schemas", filename),
+        join(process.cwd(), "packages", "core", "schemas", filename),
+    ];
+    for (const c of candidates) {
+        if (existsSync(c))
+            return c;
+    }
+    throw new Error(`Could not locate template: ${filename}`);
+}
+function formatDiff(diff) {
+    const out = [];
+    out.push(`Profile: ${diff.profileAction} -> ${diff.profilePath}`);
+    for (const cd of diff.clients) {
+        out.push(`Client ${cd.client} (${cd.action}): ${cd.path}`);
+        for (const a of cd.added)
+            out.push(`  + mcpServers.${a}`);
+        for (const c of cd.collisions)
+            out.push(`  ! mcpServers.${c} (collision)`);
+        if (cd.reason)
+            out.push(`  reason: ${cd.reason}`);
+    }
+    return out;
+}
+//# sourceMappingURL=init.js.map

package/dist/commands/init.js.map

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

@@ -0,0 +1,14 @@
+import { type ValidationResult } from "../profile/validator.js";
+export interface ValidateResult {
+    readonly path: string;
+    readonly result: ValidationResult;
+    readonly missing: boolean;
+}
+export declare function runProfileValidate(): Promise<ValidateResult>;
+export interface ShowResult {
+    readonly path: string;
+    readonly yaml: string;
+    readonly missing: boolean;
+}
+export declare function runProfileShow(): Promise<ShowResult>;
+//# sourceMappingURL=profile.d.ts.map