neotoma 0.4.2 → 0.4.5

package/dist/cli/doctor.js

@@ -0,0 +1,345 @@
+/**
+ * `neotoma doctor` — consolidated diagnostics for agent-led onboarding.
+ *
+ * Returns a single machine-readable snapshot covering install/runtime/API/MCP/
+ * CLI instructions/permission-file state so agents do not improvise with shell
+ * introspection (python3, grep, ls, cat, jq, find, which, node -e).
+ */
+import fs from "node:fs/promises";
+import { existsSync, readFileSync } from "node:fs";
+import os from "node:os";
+import path from "node:path";
+import { fileURLToPath } from "node:url";
+import { execFileSync } from "node:child_process";
+import { discoverApiInstances } from "./config.js";
+import { detectHooks, toHookHarness, } from "./hooks_detect.js";
+const __filename = fileURLToPath(import.meta.url);
+const __dirname = path.dirname(__filename);
+function safeExec(cmd, args) {
+    try {
+        const out = execFileSync(cmd, args, { stdio: ["ignore", "pipe", "ignore"], encoding: "utf8" });
+        return out.trim() || null;
+    }
+    catch {
+        return null;
+    }
+}
+/** Resolve the neotoma binary and detect which shell-manager owns node (mise/nvm/fnm). */
+function detectRuntime() {
+    const whichNeotoma = safeExec("which", ["neotoma"]);
+    const whichNode = safeExec("which", ["node"]);
+    const npmPrefix = safeExec("npm", ["prefix", "-g"]);
+    const npmRoot = npmPrefix ? path.join(npmPrefix, "lib", "node_modules") : null;
+    const globalBin = npmPrefix ? path.join(npmPrefix, "bin", "neotoma") : null;
+    const globalPkgDir = npmRoot ? path.join(npmRoot, "neotoma") : null;
+    const globalPkgExists = globalPkgDir ? existsSync(globalPkgDir) : false;
+    // Detect resolved_via from the which-neotoma path
+    let resolvedVia = "unknown";
+    if (whichNeotoma) {
+        if (whichNeotoma.includes("/.local/share/mise/") || whichNeotoma.includes("/.mise/")) {
+            resolvedVia = "mise";
+        }
+        else if (whichNeotoma.includes("/.nvm/")) {
+            resolvedVia = "nvm";
+        }
+        else if (whichNeotoma.includes("/.fnm/") || whichNeotoma.includes("/fnm/")) {
+            resolvedVia = "fnm";
+        }
+        else if (whichNeotoma.includes("/node_modules/") || (globalBin && path.resolve(whichNeotoma) === path.resolve(globalBin))) {
+            resolvedVia = "npm";
+        }
+        else {
+            resolvedVia = "path";
+        }
+    }
+    // Compute hint when `which neotoma` fails but the global package exists (typical mise/nvm PATH mismatch).
+    let pathFixHint = null;
+    if (!whichNeotoma && globalPkgExists) {
+        if (npmPrefix && npmPrefix.includes("/mise/")) {
+            pathFixHint = `Run \`eval "$(mise activate zsh)"\` in this shell (or restart the terminal) so your agent shell finds the \`neotoma\` binary at ${globalBin ?? "the global npm bin"}.`;
+        }
+        else if (npmPrefix && npmPrefix.includes("/.nvm/")) {
+            pathFixHint = `Your Node version manager (nvm) installed neotoma at ${globalBin}. Ensure your non-interactive shell sources nvm (e.g. add \`source "$NVM_DIR/nvm.sh"\` to ~/.zshenv).`;
+        }
+        else {
+            pathFixHint = `\`neotoma\` is not on PATH but exists at ${globalBin ?? globalPkgDir}. Add the containing directory to PATH or re-run \`npm install -g neotoma\` from this shell.`;
+        }
+    }
+    else if (!whichNeotoma && !globalPkgExists) {
+        pathFixHint = "Run `npm install -g neotoma` to install the CLI globally.";
+    }
+    return {
+        neotoma_on_path: Boolean(whichNeotoma),
+        node_on_path: Boolean(whichNode),
+        resolved_via: resolvedVia,
+        which_neotoma: whichNeotoma,
+        global_bin: globalBin,
+        npm_global_root: npmRoot,
+        global_package_dir: globalPkgExists ? globalPkgDir : null,
+        path_fix_hint: pathFixHint,
+    };
+}
+function readVersionFromPackageJson(pkgPath) {
+    try {
+        const raw = readFileSync(pkgPath, "utf8");
+        const pkg = JSON.parse(raw);
+        return pkg.version ?? null;
+    }
+    catch {
+        return null;
+    }
+}
+/** Detect the neotoma version from global package.json or local install. */
+function detectVersion(globalPkgDir) {
+    if (globalPkgDir) {
+        const v = readVersionFromPackageJson(path.join(globalPkgDir, "package.json"));
+        if (v)
+            return v;
+    }
+    // Fallback: package.json adjacent to current module (dev checkout)
+    try {
+        const here = path.resolve(path.join(__dirname, "..", "..", "package.json"));
+        const v = readVersionFromPackageJson(here);
+        if (v)
+            return v;
+    }
+    catch {
+        // ignore
+    }
+    return null;
+}
+/** Heuristically detect which agent harness invoked the CLI (for `current_tool_hint`). */
+function detectCurrentToolHint(cwd) {
+    const env = process.env;
+    if (env.CLAUDE_CODE_ENTRYPOINT || env.CLAUDECODE)
+        return "claude-code";
+    if (env.CURSOR_AGENT || env.CURSOR_TRACE_ID || env.CURSOR_IDE)
+        return "cursor";
+    if (env.OPENAI_CODEX_BUILD || env.CODEX_HOME)
+        return "codex";
+    if (env.OPENCLAW_SESSION || env.OPENCLAW_CWD)
+        return "openclaw";
+    // Second-best: directory-level markers.
+    try {
+        if (existsSync(path.join(cwd, ".claude")))
+            return "claude-code";
+        if (existsSync(path.join(cwd, ".cursor")))
+            return "cursor";
+        if (existsSync(path.join(cwd, ".codex")))
+            return "codex";
+    }
+    catch {
+        // ignore
+    }
+    return null;
+}
+/** Check a Claude Code permission file for neotoma wildcard allow entries. */
+async function readClaudePermissions(filePath) {
+    try {
+        const raw = await fs.readFile(filePath, "utf8");
+        const parsed = JSON.parse(raw);
+        const allow = parsed.permissions?.allow ?? [];
+        return {
+            path: filePath,
+            exists: true,
+            has_neotoma_allow: allow.some((s) => /^Bash\(neotoma:\*?\)$/.test(s) || s === "Bash(neotoma:*)"),
+            has_npm_install_allow: allow.some((s) => /npm\s+install\s+-g\s+neotoma/.test(s)),
+        };
+    }
+    catch {
+        return { path: filePath, exists: false, has_neotoma_allow: false, has_npm_install_allow: false };
+    }
+}
+/** Check a Cursor allowlist JSON file (or legacy path) for neotoma entries. */
+async function readCursorAllowlist(projectRoot) {
+    const candidate = path.join(projectRoot, ".cursor", "allowlist.json");
+    try {
+        const raw = await fs.readFile(candidate, "utf8");
+        const parsed = JSON.parse(raw);
+        const allow = parsed.allow ?? [];
+        return {
+            path: candidate,
+            exists: true,
+            has_neotoma_allow: allow.some((s) => /neotoma/.test(s)),
+            has_npm_install_allow: allow.some((s) => /npm\s+install\s+-g\s+neotoma/.test(s)),
+        };
+    }
+    catch {
+        return { path: candidate, exists: false, has_neotoma_allow: false, has_npm_install_allow: false };
+    }
+}
+/** Check Codex config.toml for neotoma approval entries. */
+async function readCodexApprovals() {
+    const home = os.homedir();
+    const candidate = path.join(home, ".codex", "config.toml");
+    try {
+        const raw = await fs.readFile(candidate, "utf8");
+        const hasNeotoma = /neotoma/i.test(raw) && /\[approvals?\]/.test(raw);
+        const hasNpmAllow = /npm\s+install\s+-g\s+neotoma/.test(raw);
+        return {
+            path: candidate,
+            exists: true,
+            has_neotoma_allow: hasNeotoma,
+            has_npm_install_allow: hasNpmAllow,
+        };
+    }
+    catch {
+        return { path: candidate, exists: false, has_neotoma_allow: false, has_npm_install_allow: false };
+    }
+}
+/** Suggest the next step based on consolidated state. */
+function suggestNextStep(report) {
+    if (!report.neotoma.installed)
+        return "install";
+    if (!report.data.initialized)
+        return "init";
+    const mcpConfigured = Object.values(report.mcp_servers_detected).some((c) => c.has_neotoma || c.has_neotoma_dev);
+    if (!mcpConfigured)
+        return "configure-mcp";
+    const cliInstr = report.cli_instructions;
+    const hasAnyCliInstr = cliInstr.project.cursor ||
+        cliInstr.project.claude ||
+        cliInstr.project.codex ||
+        cliInstr.user.cursor ||
+        cliInstr.user.claude ||
+        cliInstr.user.codex;
+    if (!hasAnyCliInstr)
+        return "configure-cli-instructions";
+    const hasPerms = Object.values(report.permission_files).some((p) => p.has_neotoma_allow);
+    if (!hasPerms && report.current_tool_hint && report.current_tool_hint !== "openclaw") {
+        return "configure-permissions";
+    }
+    if (!report.api.running)
+        return "activate";
+    if (report.hooks.eligible_for_offer)
+        return "offer-hooks";
+    return "ready";
+}
+export async function runDoctor(opts = {}) {
+    const cwd = opts.cwd ?? process.cwd();
+    const runtime = detectRuntime();
+    const version = detectVersion(runtime.global_package_dir);
+    const installed = runtime.neotoma_on_path || runtime.global_package_dir !== null;
+    // Data/init status
+    const configDir = path.join(os.homedir(), ".config", "neotoma");
+    const dataDir = process.env.NEOTOMA_DATA_DIR ?? path.join(os.homedir(), "neotoma", "data");
+    const dbCandidates = [path.join(dataDir, "neotoma.db"), path.join(dataDir, "neotoma.prod.db")];
+    const dbExists = dbCandidates.some((p) => existsSync(p));
+    const initialized = dbExists && existsSync(configDir);
+    // API running?
+    let apiRunning = false;
+    let apiEnv = null;
+    let apiPort = null;
+    const apiPid = null;
+    let apiBaseUrl = null;
+    try {
+        const instances = await discoverApiInstances({ config: opts.config });
+        const first = instances.find((i) => i.healthy) ?? instances[0];
+        if (first) {
+            apiRunning = Boolean(first.healthy);
+            apiEnv = first.envHint === "dev" ? "dev" : first.envHint === "prod" ? "prod" : null;
+            apiPort = first.port ?? null;
+            apiBaseUrl = first.url ?? null;
+        }
+    }
+    catch {
+        // ignore discovery errors
+    }
+    // MCP server detection
+    const mcpServersDetected = {};
+    try {
+        const { scanForMcpConfigs } = await import("./mcp_config_scan.js");
+        const { configs } = await scanForMcpConfigs(cwd, { includeUserLevel: true });
+        for (const c of configs) {
+            const id = inferMcpToolId(c.path);
+            mcpServersDetected[id] = {
+                path: c.path,
+                has_neotoma: c.hasProd,
+                has_neotoma_dev: c.hasDev,
+            };
+        }
+    }
+    catch {
+        // leave empty
+    }
+    // CLI instructions
+    let cliInstructions = {
+        project: { cursor: false, claude: false, codex: false },
+        user: { cursor: false, claude: false, codex: false },
+    };
+    try {
+        const { scanAgentInstructions } = await import("./agent_instructions_scan.js");
+        const res = await scanAgentInstructions(cwd, { includeUserLevel: true });
+        cliInstructions = {
+            project: {
+                cursor: res.appliedProject.cursor,
+                claude: res.appliedProject.claude,
+                codex: res.appliedProject.codex,
+            },
+            user: {
+                cursor: res.appliedUser.cursor,
+                claude: res.appliedUser.claude,
+                codex: res.appliedUser.codex,
+            },
+        };
+    }
+    catch {
+        // leave defaults
+    }
+    // Permission files
+    const permissionFiles = {
+        claude_code_project: await readClaudePermissions(path.join(cwd, ".claude", "settings.local.json")),
+        claude_code_user: await readClaudePermissions(path.join(os.homedir(), ".claude", "settings.json")),
+        cursor_project: await readCursorAllowlist(cwd),
+        codex_user: await readCodexApprovals(),
+    };
+    const currentToolHint = detectCurrentToolHint(cwd);
+    // Hooks detection. `toHookHarness` filters out tools without hook support
+    // (e.g. claude-desktop, openclaw) so eligibility never triggers on them.
+    const mcpConfigured = Object.values(mcpServersDetected).some((c) => c.has_neotoma || c.has_neotoma_dev);
+    const currentHookHarness = toHookHarness(currentToolHint);
+    const hooks = await detectHooks({
+        cwd,
+        currentTool: currentHookHarness,
+        mcpConfigured,
+    });
+    const partial = {
+        neotoma: {
+            installed,
+            version,
+            ...runtime,
+        },
+        data: {
+            config_dir: configDir,
+            data_dir: dataDir,
+            db_exists: dbExists,
+            initialized,
+        },
+        api: {
+            running: apiRunning,
+            env: apiEnv,
+            port: apiPort,
+            pid: apiPid,
+            base_url: apiBaseUrl,
+        },
+        mcp_servers_detected: mcpServersDetected,
+        cli_instructions: cliInstructions,
+        permission_files: permissionFiles,
+        current_tool_hint: currentToolHint,
+        hooks,
+    };
+    return { ...partial, suggested_next_step: suggestNextStep(partial) };
+}
+function inferMcpToolId(filePath) {
+    const n = filePath.toLowerCase();
+    if (n.includes(".cursor"))
+        return "cursor";
+    if (n.includes("claude_desktop"))
+        return "claude_desktop";
+    if (n.includes(".claude"))
+        return "claude_code";
+    if (n.includes(".codex"))
+        return "codex";
+    return path.basename(filePath);
+}
+//# sourceMappingURL=doctor.js.map

package/dist/cli/doctor.js.map

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package/dist/cli/hooks.d.ts

@@ -0,0 +1,45 @@
+/**
+ * `neotoma hooks` — install / uninstall / status for lifecycle hooks.
+ *
+ * This command intentionally does *not* ship as part of `neotoma setup`.
+ * Hooks are offered separately during activation (see install.md step 6.5)
+ * so the user sees Neotoma's MCP-driven value before we add a second write
+ * path into their tool configuration.
+ *
+ * The command itself is a thin wrapper that delegates to each package's own
+ * installer script:
+ *   - cursor   → packages/cursor-hooks/scripts/install.mjs
+ *   - codex    → packages/codex-hooks/scripts/install.mjs
+ *   - claude-code / opencode / claude-agent-sdk → print a snippet and exit
+ *
+ * Guardrails (enforced before any write):
+ *   - `data.initialized === false` → refuse; instruct user to `neotoma init`.
+ *   - `hooks.installed[tool].other_hook_plugins.length > 0` → refuse unless
+ *     `--force` is set; surface the detected plugin names.
+ *   - Non-interactive prompt by default; `--yes` bypasses confirmation.
+ */
+import { type DoctorReport } from "./doctor.js";
+import type { HookHarnessId } from "./hooks_detect.js";
+export interface HooksCommandOptions {
+    tool: HookHarnessId;
+    cwd?: string;
+    dryRun?: boolean;
+    yes?: boolean;
+    force?: boolean;
+}
+export interface HooksCommandResult {
+    ok: boolean;
+    tool: HookHarnessId;
+    action: "install" | "uninstall" | "status";
+    message: string;
+    /** Populated when delegation to a package script happened. */
+    delegated_to: string | null;
+    /** Raw doctor.hooks snapshot after the command. */
+    status: DoctorReport["hooks"];
+}
+export declare function runHooksInstall(opts: HooksCommandOptions): Promise<HooksCommandResult>;
+export declare function runHooksUninstall(opts: HooksCommandOptions): Promise<HooksCommandResult>;
+export declare function runHooksStatus(opts?: {
+    cwd?: string;
+}): Promise<DoctorReport["hooks"]>;
+//# sourceMappingURL=hooks.d.ts.map

package/dist/cli/hooks.d.ts.map

@@ -0,0 +1 @@
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