vault-cortex 0.7.0 → 0.9.0

package/README.md

@@ -15,14 +15,20 @@ and data files — see the
 The server runs as a Docker container; this CLI scaffolds the config and
 manages the container so you don't have to.
 
-![npx vault-cortex init — the interactive setup wizard picks a mode, finds your vault, generates the config, and starts the server](https://raw.githubusercontent.com/aliasunder/vault-cortex/main/assets/demo-cli-init.gif)
+![npx vault-cortex init — the interactive setup wizard picks a mode, finds your vault, offers the optional settings, generates the config, and starts the server](https://raw.githubusercontent.com/aliasunder/vault-cortex/main/assets/demo-cli-init.gif)
 
 ## Commands
 
 - [`init`](#init) — interactive setup: scaffold the config, generate the auth
   token, start the server
+- [`configure`](#configure) — change optional settings interactively and
+  restart to apply them
 - [`upgrade`](#upgrade) — pull the latest image and re-create the container;
   your data stays
+- [`restart`](#restart) — re-create the container so your `.env` edits take
+  effect; no image pull
+- [`logs`](#logs) — show the server's logs, live or after the fact
+- [`down`](#down) — stop and remove the container; your data stays
 - [`get-sync-token`](#get-sync-token) — generate an Obsidian Sync auth token
   for remote setups
 
@@ -40,9 +46,14 @@ What it does:
    - **Local** — Docker on this machine, your vault folder bind-mounted
    - **Remote** — a VPS with [Obsidian Sync](https://obsidian.md/sync),
      reachable from any device
-2. Generates a `.env` file with a securely generated `MCP_AUTH_TOKEN`
-3. Optionally starts the container and waits for the health check
-4. Prints your connection details — the MCP URL, your auth token, and how to
+2. Offers the most common optional settings — memory layer and folder,
+   file tools, semantic search, port, timezone (plus sync direction for
+   remote) — press enter to keep the defaults, or pick the ones you want to
+   change. Skipped when the target directory already has a `.env` (use
+   [`configure`](#configure) instead)
+3. Generates a `.env` file with a securely generated `MCP_AUTH_TOKEN`
+4. Optionally starts the container and waits for the health check
+5. Prints your connection details — the MCP URL, your auth token, and how to
    connect your client
 
 Existing files are never overwritten without asking. During a remote setup,
@@ -63,6 +74,22 @@ Non-interactive example:
 npx vault-cortex@latest init --yes --vault-path /path/to/YourVault
 ```
 
+## configure
+
+Change optional settings on an existing setup:
+
+```bash
+npx vault-cortex@latest configure
+```
+
+Shows the same settings chooser as [`init`](#init) — memory layer and
+folder, file tools, semantic search, port, timezone (plus sync direction
+for remote) — pre-filled with your current values, saves your picks to
+`.env`, and offers to restart the container so they take effect. Settings not in the chooser
+live in `.env` too: edit the value there, then run [`restart`](#restart).
+
+Use `--dir <path>` if your config isn't in `./vault-cortex`.
+
 ## upgrade
 
 Pull the latest image, re-create the container, and verify health:
@@ -88,6 +115,55 @@ include Compose files you can use directly. If you set up with Compose, stick
 with Compose for updates too (`docker compose pull && docker compose up -d`)
 — the CLI and Compose manage the container independently.
 
+## restart
+
+Re-create the container from your `.env` and verify health:
+
+```bash
+npx vault-cortex@latest restart
+```
+
+Use it after editing `.env` — settings are only read when the container is
+created, so a plain `docker restart` won't pick them up, but this will. Unlike
+[`upgrade`](#upgrade), it never pulls a new image: you get the same server
+version back, with your current settings applied.
+
+Use `--dir <path>` if your config isn't in `./vault-cortex`.
+
+## logs
+
+Show the server's logs:
+
+```bash
+npx vault-cortex@latest logs
+```
+
+Flags:
+
+- `--follow` — keep streaming new output until you press ctrl-C
+- `--since <time>` — only logs newer than this (e.g. `10m`, `2h`, or a
+  timestamp)
+- `--dir <path>` — directory containing `.env` (default `./vault-cortex`)
+
+```bash
+npx vault-cortex@latest logs --follow --since 10m
+```
+
+## down
+
+Stop and remove the container:
+
+```bash
+npx vault-cortex@latest down
+```
+
+Safe by design: your vault, search index, and `.env` settings all live
+outside the container, so nothing is lost. Start again any time with
+[`restart`](#restart). Running `down` when nothing is running is fine — it
+just tells you there's nothing to stop.
+
+Use `--dir <path>` if your config isn't in `./vault-cortex`.
+
 ## get-sync-token
 
 Generate an [Obsidian Sync](https://obsidian.md/sync) auth token — needed for

package/dist/configure.js

@@ -0,0 +1,64 @@
+import { readFileSync, writeFileSync } from "node:fs";
+import { recreateContainer, requireInitializedDir, resolveDeployment, } from "./lifecycle.js";
+import { applyOptionalSettings, askOptionalSettings, derivePublicUrlOverride, readOptionalValue, } from "./optional-settings.js";
+/**
+ * Interactively changes optional settings in an existing deployment's .env,
+ * then offers to re-create the container so the new values take effect (the
+ * env-file is only read at container creation). The edit succeeds on its own:
+ * a stopped daemon or a declined restart still exits 0 with the settings
+ * saved and a restart hint printed.
+ */
+export const runConfigure = async (flags, deps) => {
+    const { prompts, docker, fetchFn } = deps;
+    prompts.intro("vault-cortex configure");
+    // Editing settings only needs an init'd .env — the full start validation
+    // (VAULT_PATH, PUBLIC_URL) runs later, only when a restart is requested.
+    const initialized = requireInitializedDir(flags.dir, prompts);
+    if (!initialized)
+        return 1;
+    const { targetDir, envFilePath, mode } = initialized;
+    const envContent = readFileSync(envFilePath, "utf8");
+    const pickedOverrides = await askOptionalSettings({ mode, envContent }, prompts);
+    if (Object.keys(pickedOverrides).length === 0) {
+        prompts.log("No settings selected — nothing changed.");
+        prompts.outro("Done.");
+        return 0;
+    }
+    const overrides = derivePublicUrlOverride(envContent, pickedOverrides);
+    const changedNames = Object.keys(overrides);
+    writeFileSync(envFilePath, applyOptionalSettings(envContent, overrides));
+    prompts.log(`Updated ${changedNames.join(", ")} in ${targetDir}/.env.`);
+    // A custom PUBLIC_URL is never rewritten (see derivePublicUrlOverride), but
+    // a port change can still strand it — surface the consequence non-blocking.
+    const currentPublicUrl = readOptionalValue(envContent, "PUBLIC_URL");
+    if (pickedOverrides.PORT && !overrides.PUBLIC_URL && currentPublicUrl) {
+        prompts.warn(`PORT changed — make sure PUBLIC_URL (${currentPublicUrl}) still reaches the server.`);
+    }
+    const restartHint = `Apply the new settings with: npx vault-cortex restart --dir "${targetDir}"`;
+    if (!docker.isDaemonRunning()) {
+        prompts.warn(`Container runtime not running — settings saved.\n${restartHint}`);
+        prompts.outro("Done.");
+        return 0;
+    }
+    const restartNow = await prompts.confirm("Restart the container now to apply the new settings?", true);
+    if (!restartNow) {
+        prompts.log(restartHint);
+        prompts.outro("Done.");
+        return 0;
+    }
+    // Resolve from disk after the write so the restart honors the new values
+    // (a changed PORT must drive the port mapping and health URL).
+    const deployment = resolveDeployment(flags.dir, prompts);
+    if (!deployment) {
+        // The edit already succeeded — don't let the failed restart read as a
+        // failed configure.
+        prompts.warn(`The restart did not run — your settings are saved. Fix the issue above, then apply them with: npx vault-cortex restart --dir "${targetDir}"`);
+        return 1;
+    }
+    const exitCode = await recreateContainer({ deployment, healthTimeoutMs: deps.healthTimeoutMs }, { prompts, docker, fetchFn });
+    if (exitCode !== 0)
+        return exitCode;
+    prompts.log("Applied the current .env settings.");
+    prompts.outro("Configure complete.");
+    return 0;
+};

package/dist/docker.js

@@ -1,4 +1,4 @@
-import { spawnSync } from "node:child_process";
+import { spawn, spawnSync } from "node:child_process";
 export const LOCAL_IMAGE = "ghcr.io/aliasunder/vault-cortex:latest";
 export const REMOTE_IMAGE = "ghcr.io/aliasunder/vault-cortex:remote";
 export const CONTAINER_NAME = "vault-cortex";
@@ -94,6 +94,19 @@ export const buildDockerRunArgs = (params) => {
     args.push(image);
     return args;
 };
+/**
+ * Builds the `docker logs` args array. Pure function — no I/O — so it's
+ * testable without spawning processes.
+ */
+export const buildDockerLogsArgs = (params) => {
+    const { follow, since } = params;
+    return [
+        "logs",
+        ...(follow ? ["--follow"] : []),
+        ...(since ? ["--since", since] : []),
+        CONTAINER_NAME,
+    ];
+};
 export const createDockerRunner = () => ({
     isDaemonRunning: () => spawnSync("docker", ["info"], { timeout: 5_000 }).status === 0,
     // stdout is discarded: `docker run -d` prints only the container ID there,
@@ -108,6 +121,33 @@ export const createDockerRunner = () => ({
     }).status === 0,
     pullImage: (image) => spawnSync("docker", ["pull", image], { stdio: "inherit" }).status === 0,
     stopAndRemoveContainer: () => spawnSync("docker", ["rm", "-f", CONTAINER_NAME]).status === 0,
+    // `docker rm -f` on a missing container exits 1 on engines < 23 and 0 on
+    // >= 23, so stopAndRemoveContainer's status can't distinguish "already
+    // gone" from "failed" — callers needing idempotent messaging probe
+    // existence first. Output stays piped (discarded): this is a boolean probe.
+    containerExists: () => spawnSync("docker", ["container", "inspect", CONTAINER_NAME]).status === 0,
+    // Async spawn, not spawnSync: --follow streams until interrupted, and the
+    // exit code must be observable after the stream closes.
+    streamLogs: (params) => new Promise((resolveExitCode) => {
+        const child = spawn("docker", buildDockerLogsArgs(params), {
+            stdio: ["ignore", "inherit", "inherit"],
+        });
+        // ctrl-C delivers SIGINT to the whole foreground process group. Node's
+        // default disposition would kill this process before the child's
+        // "close" event fires; this no-op keep-alive lets the docker child
+        // exit on its own SIGINT, the streams flush, and the exit code
+        // propagate. `once` self-removes, so later ctrl-Cs behave normally.
+        process.once("SIGINT", () => { });
+        child.once("error", (spawnError) => {
+            // Event handler, not a catch — but the same "never swallow" rule
+            // applies: without this line a spawn failure is a bare exit 1.
+            process.stderr.write(`vault-cortex: could not run docker logs — ${spawnError.message}\n`);
+            resolveExitCode(1);
+        });
+        // A null code means the child died to a signal — report the shell
+        // convention for ctrl-C (128 + SIGINT = 130).
+        child.once("close", (code) => resolveExitCode(code ?? 130));
+    }),
     runObsidianLogin: (configMountPath) => spawnSync("docker", buildObsidianLoginArgs({
         configMountPath,
         uid: process.getuid?.(),

package/dist/env.js

@@ -10,9 +10,10 @@
 // └─────────────────────────────────────────────────────────────────────────┘
 // sync:local-optional:begin
 const LOCAL_OPTIONAL_BLOCK = `# Optional ──────────────────────────────────────────────────
-# To change a setting: edit its value (uncommenting it first if needed),
-# then apply with "npx vault-cortex upgrade" (restart alone does not
-# re-read this file).
+# To change a setting: run "npx vault-cortex configure", or edit its
+# value here (uncommenting it first if needed) and apply with
+# "npx vault-cortex restart" (plain docker restart does not re-read
+# this file).
 
 # Public URL for OAuth issuer URL in discovery metadata (default: http://localhost:8000).
 # Override if you expose the server on a different URL (e.g. via a reverse proxy).
@@ -100,9 +101,10 @@ WINDOWS_MODE=false
 // └─────────────────────────────────────────────────────────────────────────┘
 // sync:remote-optional:begin
 const REMOTE_OPTIONAL_BLOCK = `# Optional ──────────────────────────────────────────────────
-# To change a setting: edit its value (uncommenting it first if needed),
-# then apply with "npx vault-cortex upgrade" (restart alone does not
-# re-read this file).
+# To change a setting: run "npx vault-cortex configure", or edit its
+# value here (uncommenting it first if needed) and apply with
+# "npx vault-cortex restart" (plain docker restart does not re-read
+# this file).
 
 # Your IANA timezone — affects daily note resolution and memory timestamps.
 # TZ=America/New_York
@@ -204,10 +206,6 @@ MCP_AUTH_TOKEN=${answers.mcpAuthToken}
 # Absolute path to your Obsidian vault on this machine.
 VAULT_PATH=${answers.vaultPath}
 
-# Public URL for OAuth issuer URL in discovery metadata.
-# Override if you expose the server on a different URL (e.g. via a reverse proxy).
-PUBLIC_URL=http://localhost:8000
-
 ${LOCAL_OPTIONAL_BLOCK}`;
 export const buildRemoteEnv = (answers) => {
     const vaultPasswordLines = answers.vaultPassword === undefined

package/dist/init.js

@@ -1,8 +1,10 @@
+import { existsSync } from "node:fs";
 import { join, resolve } from "node:path";
 import { buildLocalEnv, buildRemoteEnv } from "./env.js";
 import { captureObsidianToken } from "./get-sync-token.js";
 import { buildLocalConnectMessage, buildRemoteConnectMessage, } from "./messages.js";
 import { pollHealth } from "./docker.js";
+import { applyOptionalSettings, askOptionalSettings, derivePublicUrlOverride, } from "./optional-settings.js";
 import { buildFilesToWrite, readEnvPort, writeFiles, } from "./scaffold.js";
 import { generateToken } from "./token.js";
 import { expandTilde, validateVaultPath } from "./vault.js";
@@ -203,10 +205,25 @@ const runLocalInit = async (flags, deps) => {
                 placeholder: DEFAULT_TARGET_DIR,
             }))));
     const token = generateToken();
+    // Guided optional settings: the chooser reads current values from the
+    // generated defaults; enter with nothing picked keeps them all. --yes
+    // skips the chooser (non-interactive by contract), and so does an existing
+    // .env — the conflict prompt defaults to keeping it, which would discard
+    // the answers; settings on an existing deployment are configure's job.
+    const defaultEnvContent = buildLocalEnv({ mcpAuthToken: token, vaultPath });
+    const envAlreadyExists = existsSync(join(targetDir, ".env"));
+    const offerSettingsChooser = !flags.yes && !envAlreadyExists;
+    if (!flags.yes && envAlreadyExists) {
+        prompts.log('Found an existing .env — settings prompts skipped. Adjust settings with "npx vault-cortex configure".');
+    }
+    const optionalOverrides = offerSettingsChooser
+        ? await askOptionalSettings({ mode: "local", envContent: defaultEnvContent }, prompts)
+        : {};
+    const envContent = applyOptionalSettings(defaultEnvContent, derivePublicUrlOverride(defaultEnvContent, optionalOverrides));
     // Conflict policy: identical existing files are skipped silently;
     // differing ones prompt per file (default keep). --yes never overwrites —
     // any differing file becomes an exit-1 below, leaving it untouched.
-    const files = buildFilesToWrite(buildLocalEnv({ mcpAuthToken: token, vaultPath }));
+    const files = buildFilesToWrite(envContent);
     const resolveConflict = flags.yes ? keepExisting : confirmOverwrite(prompts);
     const results = await writeFiles({ targetDir, files }, resolveConflict);
     reportWrites({ targetDir, results }, prompts);
@@ -262,13 +279,24 @@ const runRemoteInit = async (flags, deps) => {
         ? await prompts.password("Vault encryption password:")
         : undefined;
     const token = generateToken();
-    const envContent = buildRemoteEnv({
+    // Guided optional settings, mirroring the local flow — remote also offers
+    // SYNC_MODE. Remote init is always interactive (no --yes), so only an
+    // existing .env skips the chooser here.
+    const defaultEnvContent = buildRemoteEnv({
         mcpAuthToken: token,
         publicUrl,
         obsidianAuthToken,
         vaultName,
         vaultPassword,
     });
+    const envAlreadyExists = existsSync(join(targetDir, ".env"));
+    if (envAlreadyExists) {
+        prompts.log('Found an existing .env — settings prompts skipped. Adjust settings with "npx vault-cortex configure".');
+    }
+    const optionalOverrides = envAlreadyExists
+        ? {}
+        : await askOptionalSettings({ mode: "remote", envContent: defaultEnvContent }, prompts);
+    const envContent = applyOptionalSettings(defaultEnvContent, derivePublicUrlOverride(defaultEnvContent, optionalOverrides));
     const files = buildFilesToWrite(envContent);
     const results = await writeFiles({ targetDir, files }, confirmOverwrite(prompts));
     reportWrites({ targetDir, results }, prompts);

package/dist/lifecycle.js

@@ -0,0 +1,166 @@
+import { join, resolve } from "node:path";
+import { CONTAINER_NAME, pollHealth } from "./docker.js";
+import { detectMode, hasEnvPublicUrl, readEnvPort, readEnvVaultPath, } from "./scaffold.js";
+import { expandTilde } from "./vault.js";
+const DEFAULT_TARGET_DIR = "./vault-cortex";
+/**
+ * Light gate for commands that operate on an existing deployment without
+ * starting a container: resolves --dir and confirms an init'd .env exists.
+ * Full start-readiness validation lives in resolveDeployment.
+ */
+export const requireInitializedDir = (dirFlag, prompts) => {
+    const targetDir = resolve(expandTilde(dirFlag ?? DEFAULT_TARGET_DIR));
+    const envFilePath = join(targetDir, ".env");
+    const mode = detectMode(envFilePath);
+    if (!mode) {
+        prompts.error(`No .env found in ${targetDir} — run \`npx vault-cortex init\` first.`);
+        return undefined;
+    }
+    return { targetDir, envFilePath, mode };
+};
+/**
+ * Resolves --dir to the on-disk deployment and validates its .env for a
+ * container start: mode detection, VAULT_PATH (local), and PUBLIC_URL
+ * (local). Reports each failure via prompts.error and returns undefined.
+ * Shared by upgrade and restart so their precondition checks can't drift.
+ */
+export const resolveDeployment = (dirFlag, prompts) => {
+    const initialized = requireInitializedDir(dirFlag, prompts);
+    if (!initialized)
+        return undefined;
+    const { targetDir, envFilePath, mode } = initialized;
+    const port = readEnvPort(envFilePath);
+    const vaultPath = mode === "local" ? readEnvVaultPath(envFilePath) : undefined;
+    if (mode === "local" && !vaultPath) {
+        prompts.error(`VAULT_PATH is empty or missing in ${targetDir}/.env — cannot start the container.`);
+        return undefined;
+    }
+    if (mode === "local" && !hasEnvPublicUrl(envFilePath)) {
+        prompts.error(`PUBLIC_URL not found in ${targetDir}/.env — the server requires it.\n` +
+            `Add this line to your .env:\n  PUBLIC_URL=http://localhost:${port}`);
+        return undefined;
+    }
+    return { mode, targetDir, envFilePath, port, vaultPath };
+};
+/**
+ * Verifies the container runtime is reachable, reporting the shared error
+ * message when it isn't. Callers early-return on false.
+ */
+export const ensureDaemonRunning = (docker, prompts) => {
+    if (docker.isDaemonRunning())
+        return true;
+    prompts.error("Container runtime not running — start Docker Desktop, Colima,\n" +
+        "OrbStack, or another Docker-compatible runtime.");
+    return false;
+};
+/**
+ * Stop-and-remove → docker run → health poll, with the shared messaging.
+ * Returns a process exit code. Callers own the daemon check and any
+ * image-pull step.
+ */
+export const recreateContainer = async (params, deps) => {
+    const { deployment, healthTimeoutMs } = params;
+    const { prompts, docker, fetchFn } = deps;
+    // `docker rm -f` on a missing container exits non-zero on engines < 23,
+    // so the bare return value can't distinguish "nothing to remove" from a
+    // real failure — only treat removal as failed when a container exists.
+    // Proceeding after a genuine failure would surface as a confusing
+    // "container name already in use" from docker run.
+    if (docker.containerExists() && !docker.stopAndRemoveContainer()) {
+        prompts.error(`Could not remove the existing container — check: docker rm -f ${CONTAINER_NAME}`);
+        return 1;
+    }
+    prompts.log("Starting container...");
+    const containerStarted = docker.dockerRun({
+        mode: deployment.mode,
+        envFilePath: deployment.envFilePath,
+        port: deployment.port,
+        vaultPath: deployment.vaultPath,
+    });
+    if (!containerStarted) {
+        prompts.error("docker run failed — see output above.");
+        return 1;
+    }
+    const spinner = prompts.spinner();
+    spinner.start("Waiting for the server to come up");
+    const healthy = await pollHealth({
+        url: `http://127.0.0.1:${deployment.port}/healthz`,
+        timeoutMs: healthTimeoutMs,
+    }, fetchFn);
+    if (!healthy) {
+        spinner.stop(`Server did not respond within 2 minutes — check: docker logs ${CONTAINER_NAME}`);
+        return 1;
+    }
+    spinner.stop("Server is up — health check passed.");
+    return 0;
+};
+/**
+ * Stops and removes the container. Vault data, the search index, and .env
+ * settings all live outside the container (bind mount, named volumes, host
+ * file), so this is always safe.
+ */
+export const runDown = async (flags, deps) => {
+    const { prompts, docker } = deps;
+    prompts.intro("vault-cortex down");
+    // Teardown only needs to confirm this is an init'd directory — the full
+    // .env validation (VAULT_PATH, PUBLIC_URL) guards container starts.
+    const initialized = requireInitializedDir(flags.dir, prompts);
+    if (!initialized)
+        return 1;
+    if (!ensureDaemonRunning(docker, prompts))
+        return 1;
+    if (!docker.containerExists()) {
+        prompts.log("No vault-cortex container found — nothing to stop.");
+        prompts.outro("Done.");
+        return 0;
+    }
+    if (!docker.stopAndRemoveContainer()) {
+        prompts.error(`Could not remove the container — check: docker rm -f ${CONTAINER_NAME}`);
+        return 1;
+    }
+    prompts.log("Container stopped and removed. Your vault data, search index, and settings are untouched.");
+    prompts.outro(`Start again with: npx vault-cortex restart --dir "${initialized.targetDir}"`);
+    return 0;
+};
+/**
+ * Streams `docker logs` for the vault-cortex container. The stream's exit
+ * code passes through as the command's exit code; no outro follows the raw
+ * docker output.
+ */
+export const runLogs = async (flags, deps) => {
+    const { prompts, docker } = deps;
+    prompts.intro("vault-cortex logs");
+    const initialized = requireInitializedDir(flags.dir, prompts);
+    if (!initialized)
+        return 1;
+    if (!ensureDaemonRunning(docker, prompts))
+        return 1;
+    if (!docker.containerExists()) {
+        prompts.error("No vault-cortex container — start it with `npx vault-cortex restart`.");
+        return 1;
+    }
+    return await docker.streamLogs({
+        follow: Boolean(flags.follow),
+        since: flags.since,
+    });
+};
+/**
+ * Re-creates the container from the .env on disk and verifies health.
+ * Unlike `docker restart`, this applies .env edits (the env-file is only
+ * read at container creation); unlike upgrade, it never pulls an image.
+ */
+export const runRestart = async (flags, deps) => {
+    const { prompts, docker, fetchFn } = deps;
+    prompts.intro("vault-cortex restart");
+    const deployment = resolveDeployment(flags.dir, prompts);
+    if (!deployment)
+        return 1;
+    if (!ensureDaemonRunning(docker, prompts))
+        return 1;
+    const exitCode = await recreateContainer({ deployment, healthTimeoutMs: deps.healthTimeoutMs }, { prompts, docker, fetchFn });
+    if (exitCode !== 0)
+        return exitCode;
+    prompts.log("Applied the current .env settings.");
+    prompts.outro("Restart complete.");
+    return 0;
+};

package/dist/main.js

@@ -1,6 +1,8 @@
+import { runConfigure } from "./configure.js";
 import { createDockerRunner } from "./docker.js";
 import { runGetSyncToken } from "./get-sync-token.js";
 import { runInit } from "./init.js";
+import { runDown, runLogs, runRestart } from "./lifecycle.js";
 import { buildProgram } from "./program.js";
 import { createPrompts } from "./prompts.js";
 import { runUpgrade } from "./upgrade.js";
@@ -12,11 +14,29 @@ export const run = async (version) => {
             docker: createDockerRunner(),
             fetchFn: fetch,
         }),
+        runConfigure: (flags) => runConfigure(flags, {
+            prompts: createPrompts(),
+            docker: createDockerRunner(),
+            fetchFn: fetch,
+        }),
         runUpgrade: (flags) => runUpgrade(flags, {
             prompts: createPrompts(),
             docker: createDockerRunner(),
             fetchFn: fetch,
         }),
+        runRestart: (flags) => runRestart(flags, {
+            prompts: createPrompts(),
+            docker: createDockerRunner(),
+            fetchFn: fetch,
+        }),
+        runLogs: (flags) => runLogs(flags, {
+            prompts: createPrompts(),
+            docker: createDockerRunner(),
+        }),
+        runDown: (flags) => runDown(flags, {
+            prompts: createPrompts(),
+            docker: createDockerRunner(),
+        }),
         runGetSyncToken: (flags) => runGetSyncToken(flags, {
             prompts: createPrompts(),
             docker: createDockerRunner(),

package/dist/messages.js

@@ -110,9 +110,13 @@ ${smokeTest(`${baseUrl}/healthz`)}
 
 ${sectionRule("Settings")}
 
-Optional settings (timezone, memory folder, port, logging) are commented
-out in ${targetDir}/.env — uncomment, set a value, then apply with
-"npx vault-cortex upgrade" (restart alone does not re-read .env).
+Adjust optional settings (memory layer and folder, file tools,
+semantic search, port, timezone):
+  npx vault-cortex configure --dir "${targetDir}"
+
+Or edit ${targetDir}/.env directly — change a value (uncommenting it
+first if needed), then apply with "npx vault-cortex restart" (plain
+docker restart does not re-read .env).
 
 ${updateGuidance(targetDir)}
 
@@ -171,10 +175,13 @@ ${smokeTest(`${publicUrl}/healthz`)}
 
 ${sectionRule("Settings")}
 
-Optional settings (timezone, memory folder, port, logging, sync
-behavior) are commented out in ${targetDir}/.env — uncomment, set a
-value, then apply with "npx vault-cortex upgrade" (restart alone does
-not re-read .env).
+Adjust optional settings (memory layer and folder, file tools,
+semantic search, port, timezone, sync direction):
+  npx vault-cortex configure --dir "${targetDir}"
+
+Or edit ${targetDir}/.env directly — change a value (uncommenting it
+first if needed), then apply with "npx vault-cortex restart" (plain
+docker restart does not re-read .env).
 
 ${updateGuidance(targetDir)}
 

package/dist/optional-settings.js

@@ -0,0 +1,233 @@
+import { DEFAULT_PORT } from "./scaffold.js";
+// The curated prompt set — settings users most often want without reading
+// .env comments. Everything else stays documented-only in the generated
+// optional block, deliberately: every extra prompt costs init flow length.
+const OPTIONAL_SETTINGS = [
+    {
+        kind: "toggle",
+        name: "MEMORY_ENABLED",
+        label: "Memory layer",
+        question: "Enable the memory layer (About Me/ folder + memory tools)?",
+    },
+    {
+        kind: "folder",
+        name: "MEMORY_DIR",
+        label: "Memory folder",
+        question: "Vault folder for the memory files:",
+        defaultValue: "About Me",
+        requiresToggle: "MEMORY_ENABLED",
+    },
+    {
+        kind: "toggle",
+        name: "FILE_TOOLS_ENABLED",
+        label: "File tools",
+        question: "Enable file tools (read images, PDFs, and other non-Markdown files)?",
+    },
+    {
+        kind: "toggle",
+        name: "EMBEDDING_ENABLED",
+        label: "Semantic search",
+        question: "Enable semantic search embeddings (richer search, slower first startup)?",
+    },
+    { kind: "port", name: "PORT", label: "Host port" },
+    { kind: "timezone", name: "TZ", label: "Timezone" },
+    {
+        kind: "choice",
+        name: "SYNC_MODE",
+        label: "Sync direction",
+        question: "Obsidian Sync direction:",
+        choices: [
+            {
+                value: "bidirectional",
+                label: "Bidirectional",
+                hint: "pull remote changes and push server-side edits",
+            },
+            {
+                value: "pull-only",
+                label: "Pull-only",
+                hint: "receive changes but never push",
+            },
+            {
+                value: "push-only",
+                label: "Push-only",
+                hint: "push changes but never pull",
+            },
+        ],
+        defaultValue: "bidirectional",
+        remoteOnly: true,
+    },
+];
+/** Matches the full active (uncommented) assignment line for a var. */
+const activeLinePattern = (name) => new RegExp(`^${name}=.*$`, "m");
+/** Matches the full commented-out assignment line (`# VAR=...`) for a var. */
+const commentedLinePattern = (name) => new RegExp(`^# ${name}=.*$`, "m");
+/**
+ * Reads a var's current value from .env content. A commented-out or missing
+ * line returns undefined — both mean "the server uses its built-in default",
+ * which is exactly what the prompts need to distinguish. Duplicate lines
+ * report the LAST value, matching docker --env-file precedence — hints,
+ * prompt seeding, and the PUBLIC_URL derivation must reason from the value
+ * that actually takes effect.
+ */
+export const readOptionalValue = (envContent, name) => {
+    const matches = [...envContent.matchAll(new RegExp(`^${name}=(.*)$`, "gm"))];
+    return matches.at(-1)?.[1].trim();
+};
+/**
+ * Applies chosen values to .env content as a pure text transform: every
+ * active line for the var is replaced (docker --env-file gives the last
+ * duplicate precedence, so a single-line replace could leave a stale
+ * duplicate winning), a commented-out line is uncommented and replaced, and
+ * a var with no line at all (a .env predating the setting) is appended —
+ * the chosen value must land in the file, never be silently dropped.
+ */
+export const applyOptionalSettings = (envContent, overrides) => Object.entries(overrides).reduce((content, [name, value]) => {
+    // Fresh RegExp per use (the /g flag makes instances stateful via
+    // lastIndex); function replacements avoid $-pattern interpretation in
+    // values, same as patchEnvObsidianToken.
+    const everyActiveLine = new RegExp(`^${name}=.*$`, "gm");
+    if (activeLinePattern(name).test(content)) {
+        return content.replace(everyActiveLine, () => `${name}=${value}`);
+    }
+    if (commentedLinePattern(name).test(content)) {
+        return content.replace(commentedLinePattern(name), () => `${name}=${value}`);
+    }
+    return `${content.trimEnd()}\n\n${name}=${value}\n`;
+}, envContent);
+/**
+ * A PORT override moves the server, and the local quickstart derives
+ * PUBLIC_URL (the OAuth issuer) from that port. When the current PUBLIC_URL
+ * is exactly the derived http://localhost:<current port> form, it follows
+ * the new port — otherwise the advertised OAuth discovery endpoints would
+ * point at a port nothing listens on. A custom PUBLIC_URL (reverse proxy,
+ * remote domain) is the user's own and is never touched.
+ */
+export const derivePublicUrlOverride = (envContent, overrides) => {
+    const newPort = overrides.PORT;
+    if (!newPort)
+        return overrides;
+    const currentPort = readOptionalValue(envContent, "PORT") ?? String(DEFAULT_PORT);
+    const currentPublicUrl = readOptionalValue(envContent, "PUBLIC_URL");
+    if (currentPublicUrl !== `http://localhost:${currentPort}`)
+        return overrides;
+    return { ...overrides, PUBLIC_URL: `http://localhost:${newPort}` };
+};
+/**
+ * The .env spellings the server reads as "off" — env-var's asBool accepts
+ * 0/1 alongside true/false. An absent or unrecognized value falls to the
+ * server default, which is enabled for every curated toggle.
+ */
+const isDisabledToggleValue = (value) => ["false", "0"].includes((value ?? "").toLowerCase());
+/**
+ * Plain digits in the TCP port range. Number() coercion is not enough:
+ * it accepts "1e4"/"0x1F40"/"+9000", which readEnvPort's /^PORT=(\d+)/
+ * would later fail to read back — silently falling to the default port.
+ */
+const isValidPort = (value) => {
+    if (!/^\d+$/.test(value))
+        return false;
+    const port = Number(value);
+    return port >= 1 && port <= 65535;
+};
+/**
+ * The engine's own IANA zone validation: Intl.DateTimeFormat throws a
+ * RangeError for an unknown timeZone, so no hand-rolled zone list to drift.
+ */
+const isValidTimezone = (value) => {
+    try {
+        new Intl.DateTimeFormat("en-US", { timeZone: value });
+        return true;
+    }
+    catch {
+        return false;
+    }
+};
+/** Re-prompts until the answer is a valid port number. */
+const askPort = async (currentValue, prompts) => {
+    const answer = (await prompts.text("Host port for the server:", {
+        defaultValue: currentValue ?? String(DEFAULT_PORT),
+        placeholder: String(DEFAULT_PORT),
+    })).trim();
+    if (isValidPort(answer))
+        return answer;
+    prompts.error("PORT must be a whole number between 1 and 65535.");
+    return askPort(currentValue, prompts);
+};
+/** Re-prompts until the answer is a zone the runtime recognizes. */
+const askTimezone = async (currentValue, prompts) => {
+    const answer = (await prompts.text("Your IANA timezone:", {
+        defaultValue: currentValue,
+        placeholder: "America/New_York",
+    })).trim();
+    if (answer !== "" && isValidTimezone(answer))
+        return answer;
+    prompts.error(`"${answer}" is not a recognized IANA timezone (e.g. America/New_York, Europe/London).`);
+    return askTimezone(currentValue, prompts);
+};
+/** Re-prompts until the answer is a non-empty folder name. */
+const askFolder = async (params, prompts) => {
+    const { question, currentValue, defaultValue } = params;
+    const answer = (await prompts.text(question, {
+        defaultValue: currentValue ?? defaultValue,
+        placeholder: defaultValue,
+    })).trim();
+    if (answer !== "")
+        return answer;
+    prompts.error("The folder name can't be empty.");
+    return askFolder(params, prompts);
+};
+/** Routes a picked setting to its kind's prompt and returns the .env value. */
+const askSettingValue = async (params, prompts) => {
+    const { setting, currentValue } = params;
+    switch (setting.kind) {
+        case "toggle": {
+            const enabled = await prompts.confirm(setting.question, !isDisabledToggleValue(currentValue));
+            return String(enabled);
+        }
+        case "port":
+            return askPort(currentValue, prompts);
+        case "timezone":
+            return askTimezone(currentValue, prompts);
+        case "folder":
+            return askFolder({
+                question: setting.question,
+                currentValue,
+                defaultValue: setting.defaultValue,
+            }, prompts);
+        case "choice":
+            return prompts.select(setting.question, setting.choices, currentValue ?? setting.defaultValue);
+    }
+};
+/**
+ * The guided optional-settings flow shared by init and configure: one
+ * multiselect chooser (enter with nothing picked = change nothing), then one
+ * prompt per picked setting. Returns the chosen values keyed by var name —
+ * the caller owns applying them via applyOptionalSettings.
+ */
+export const askOptionalSettings = async (params, prompts) => {
+    const { mode, envContent } = params;
+    const offeredSettings = OPTIONAL_SETTINGS.filter((setting) => !setting.remoteOnly || mode === "remote");
+    const chooserOptions = offeredSettings.map((setting) => {
+        const currentValue = readOptionalValue(envContent, setting.name);
+        const requiredToggle = OPTIONAL_SETTINGS.find((candidate) => candidate.name === setting.requiresToggle);
+        const dependencyNote = requiredToggle &&
+            isDisabledToggleValue(readOptionalValue(envContent, requiredToggle.name))
+            ? ` · not used while ${requiredToggle.label} is off`
+            : "";
+        return {
+            value: setting.name,
+            label: setting.label,
+            hint: `${setting.name} · currently ${currentValue || "not set"}${dependencyNote}`,
+        };
+    });
+    const pickedNames = await prompts.multiselect("Any optional settings to change? (press enter to skip)", chooserOptions);
+    // Sequential prompting: answers are gathered one at a time in the curated
+    // order, so the record builds up inside an honest loop.
+    const overrides = {};
+    for (const setting of offeredSettings) {
+        if (!pickedNames.includes(setting.name))
+            continue;
+        overrides[setting.name] = await askSettingValue({ setting, currentValue: readOptionalValue(envContent, setting.name) }, prompts);
+    }
+    return overrides;
+};

package/dist/program.js

@@ -15,6 +15,13 @@ export const buildProgram = (options) => {
         .action(async (flags) => {
         process.exitCode = await options.runInit(flags);
     });
+    program
+        .command("configure")
+        .description("Change optional settings interactively and restart to apply them")
+        .option("--dir <path>", "directory containing .env (default: ./vault-cortex)")
+        .action(async (flags) => {
+        process.exitCode = await options.runConfigure(flags);
+    });
     program
         .command("upgrade")
         .description("Pull the latest image, re-create the container, and verify health")
@@ -22,6 +29,29 @@ export const buildProgram = (options) => {
         .action(async (flags) => {
         process.exitCode = await options.runUpgrade(flags);
     });
+    program
+        .command("restart")
+        .description("Re-create the container from .env and verify health (applies .env edits; no image pull)")
+        .option("--dir <path>", "directory containing .env (default: ./vault-cortex)")
+        .action(async (flags) => {
+        process.exitCode = await options.runRestart(flags);
+    });
+    program
+        .command("logs")
+        .description("Show container logs")
+        .option("--dir <path>", "directory containing .env (default: ./vault-cortex)")
+        .option("--follow", "stream new log output until interrupted (ctrl-C)")
+        .option("--since <time>", 'only logs newer than this (e.g. "10m", "2h", or a timestamp)')
+        .action(async (flags) => {
+        process.exitCode = await options.runLogs(flags);
+    });
+    program
+        .command("down")
+        .description("Stop and remove the container — vault data and settings are preserved")
+        .option("--dir <path>", "directory containing .env (default: ./vault-cortex)")
+        .action(async (flags) => {
+        process.exitCode = await options.runDown(flags);
+    });
     program
         .command("get-sync-token")
         .description("Generate an Obsidian Sync auth token via Docker and print it or write it to .env")

package/dist/prompts.js

@@ -28,6 +28,9 @@ export const createPrompts = () => ({
     warn: (message) => clack.log.warn(message),
     error: (message) => clack.log.error(message),
     select: async (message, options, initialValue) => exitOnCancel(await clack.select({ message, options, initialValue })),
+    // required: false makes an empty submission legal — the Prompts contract
+    // promises "no picks" resolves to [] instead of a re-prompt loop.
+    multiselect: async (message, options) => exitOnCancel(await clack.multiselect({ message, options, required: false })),
     text: async (message, options = {}) => exitOnCancel(await clack.text({
         message,
         placeholder: options.placeholder,

package/dist/upgrade.js

@@ -1,35 +1,19 @@
-import { join, resolve } from "node:path";
-import { CONTAINER_NAME, LOCAL_IMAGE, REMOTE_IMAGE, pollHealth, } from "./docker.js";
-import { detectMode, hasEnvPublicUrl, readEnvPort, readEnvVaultPath, } from "./scaffold.js";
-import { expandTilde } from "./vault.js";
-const DEFAULT_TARGET_DIR = "./vault-cortex";
+import { LOCAL_IMAGE, REMOTE_IMAGE } from "./docker.js";
+import { ensureDaemonRunning, recreateContainer, resolveDeployment, } from "./lifecycle.js";
+/**
+ * Pulls the latest image, re-creates the container, and verifies health.
+ * The only lifecycle command that contacts the registry — restart re-creates
+ * from the image already on disk.
+ */
 export const runUpgrade = async (flags, deps) => {
     const { prompts, docker, fetchFn } = deps;
     prompts.intro("vault-cortex upgrade");
-    const targetDir = resolve(expandTilde(flags.dir ?? DEFAULT_TARGET_DIR));
-    const envFilePath = join(targetDir, ".env");
-    const mode = detectMode(envFilePath);
-    if (!mode) {
-        prompts.error(`No .env found in ${targetDir} — run \`npx vault-cortex init\` first.`);
+    const deployment = resolveDeployment(flags.dir, prompts);
+    if (!deployment)
         return 1;
-    }
-    const port = readEnvPort(envFilePath);
-    const vaultPath = mode === "local" ? readEnvVaultPath(envFilePath) : undefined;
-    if (mode === "local" && !vaultPath) {
-        prompts.error(`VAULT_PATH is empty or missing in ${targetDir}/.env — cannot start the container.`);
-        return 1;
-    }
-    if (mode === "local" && !hasEnvPublicUrl(envFilePath)) {
-        prompts.error(`PUBLIC_URL not found in ${targetDir}/.env — the server requires it.\n` +
-            `Add this line to your .env:\n  PUBLIC_URL=http://localhost:${port}`);
-        return 1;
-    }
-    const image = mode === "local" ? LOCAL_IMAGE : REMOTE_IMAGE;
-    if (!docker.isDaemonRunning()) {
-        prompts.error("Container runtime not running — start Docker Desktop, Colima,\n" +
-            "OrbStack, or another Docker-compatible runtime.");
+    const image = deployment.mode === "local" ? LOCAL_IMAGE : REMOTE_IMAGE;
+    if (!ensureDaemonRunning(docker, prompts))
         return 1;
-    }
     const spinner = prompts.spinner();
     spinner.start(`Pulling ${image}`);
     const imagePulled = docker.pullImage(image);
@@ -38,28 +22,9 @@ export const runUpgrade = async (flags, deps) => {
         return 1;
     }
     spinner.stop("Image pulled.");
-    docker.stopAndRemoveContainer();
-    prompts.log("Starting container...");
-    const containerStarted = docker.dockerRun({
-        mode,
-        envFilePath,
-        port,
-        vaultPath,
-    });
-    if (!containerStarted) {
-        prompts.error("docker run failed — see output above.");
-        return 1;
-    }
-    spinner.start("Waiting for the server to come up");
-    const healthy = await pollHealth({
-        url: `http://127.0.0.1:${port}/healthz`,
-        timeoutMs: deps.healthTimeoutMs,
-    }, fetchFn);
-    if (!healthy) {
-        spinner.stop(`Server did not respond within 2 minutes — check: docker logs ${CONTAINER_NAME}`);
-        return 1;
-    }
-    spinner.stop("Server is up — health check passed.");
+    const exitCode = await recreateContainer({ deployment, healthTimeoutMs: deps.healthTimeoutMs }, { prompts, docker, fetchFn });
+    if (exitCode !== 0)
+        return exitCode;
     prompts.log("Your vault data, search index, and settings are preserved.");
     prompts.outro("Upgrade complete.");
     return 0;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "vault-cortex",
-  "version": "0.7.0",
+  "version": "0.9.0",
   "description": "Set up a Vault Cortex MCP server for your Obsidian vault in one command: npx vault-cortex init",
   "license": "MIT",
   "type": "module",