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feat: graduate remote control, storage and the subagent model pool, and finish the tunnel stack (#306)
## Related Issue No tracked issue — this is an internal reconciliation pass. ## Problem Three experimental features were ready to graduate but still hid behind flags, the `${now}` system prompt variable was documented but no longer had a purpose, and the Remote Control tunnel stack was split between the CLI and the gateway with no way to toggle it while the server ran. Global search stayed broken after a corrupt write instead of recovering, and a background task that outlived its agent emitted stray events. ## What changed **Breaking** - Remote Control, session indexing and global search no longer need experimental flags. Session indexing and search move to a new `[database]` config section; both kill-switch environment variables lose their `_EXPERIMENTAL` prefix. - The subagent model pool is always on; `[secondary_model]` takes effect with no opt-in. - `${now}` is gone from custom system prompt templates. It renders verbatim as an unknown placeholder now, and the agent still receives the current date through the environment disclosure. **Features** - `GET` and `POST /api/v1/remote-control` start and stop Remote Control while the server runs, backed by an xstate manager with `off`/`starting`/`on`/`stopping` states. - New `packages/remote-control` workspace holds the tunnel client and its machine-wide single-instance lock, shared by the gateway and the CLI. Both `flake.nix` lists were updated; the `pnpmDeps` hash is unchanged. **Fixes** - The Remote Control banner's Local UI link carries the server token, so it opens without a second sign-in. - The tunnel gzips text, JSON, JavaScript, XML and SVG responses; it skips `206` and already-encoded bodies, drops the ETag when it compresses, and always sets `Vary: Accept-Encoding`. - Global search rebuilds its index instead of staying broken when stored data is corrupt or a write keeps failing. - A background task settling after its agent is torn down no longer emits task events. - The desktop updater falls back to the default macOS manifest when the channel argument is empty. Notable adaptations: `REMOTE_CONTROL_ALREADY_RUNNING` uses code `40939` because `40928` is already `FS_CONFLICT` here, and the late-settlement fix is placed after `tryAcquireQuiescence` rather than before the loop drain, because this codebase reworked `close()` into phase-based error collection. ## Checklist - [x] I have read the [CONTRIBUTING](https://github.com/PyModel/pythinker-code/blob/main/CONTRIBUTING.md) document. - [ ] I have linked a related issue (external PRs: the issue must have a maintainer's `/approve`). - [x] I have added tests that prove my feature works. - [x] Ran `gen-changesets` skill, or this PR needs no changeset. - [x] Ran `gen-docs` skill, or this PR needs no doc update. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **New Features** * Remote Control is generally available through CLI, web commands, and `/remote-control`. * Added runtime start/stop controls through the server API. * Secondary-model routing is available without experimental opt-in. * Added database configuration for session indexing and global search. * Tunnel responses now support gzip compression. * **Bug Fixes** * Local UI links now open with the server token. * Search indexes recover from corruption and repeated failures. * Completed background tasks no longer emit stray events. * Improved macOS artifact finalization with the default manifest. * **Breaking Changes** * Removed the `${now}` variable from custom system prompt templates. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
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‎.changeset/graduate-database-and-remote-control.md‎

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Remote Control is always available — `pythinker rc`, `pythinker web --remote-control` and `/remote-control` no longer need an experimental flag. Session indexing and global search move to the new `[database]` section: set `PYTHINKER_CODE_PERSISTENCE_MINIDB_READMODEL` (was `PYTHINKER_CODE_EXPERIMENTAL_PERSISTENCE_MINIDB_READMODEL`) and `PYTHINKER_CODE_SEARCH_WORKER` (was `PYTHINKER_CODE_EXPERIMENTAL_SEARCH_WORKER`), or `[database] base` and `[database] search` in `config.toml`.

‎.changeset/graduate-subagent-model-pool.md‎

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The subagent model pool is always available. Remove `PYTHINKER_CODE_EXPERIMENTAL_SECONDARY_MODEL` from your environment — it no longer does anything, and `[secondary_model]` takes effect with no opt-in.

‎.changeset/remote-control-local-ui-token.md‎

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The Remote Control banner's Local UI link now carries the server token, so it opens without a second sign-in.

‎.changeset/remote-control-toggle-api.md‎

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The server can now start and stop Remote Control while it runs, through `GET` and `POST /api/v1/remote-control`.

‎.changeset/remote-control-tunnel-gzip.md‎

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Remote Control now gzips text, JSON, JavaScript, XML and SVG responses over the tunnel.

‎.changeset/remove-now-template-variable.md‎

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Remove the `${now}` variable from custom system prompt templates. Delete `${now}` from your `SYSTEM.md` and agent files — the agent still receives the current date.

‎.changeset/search-index-self-heal.md‎

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Global search now rebuilds its index instead of staying broken when the stored data is corrupt or a write keeps failing.

‎.changeset/silent-late-task-settlement.md‎

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A background task that finishes after its agent is closed no longer emits stray task events.

‎AGENTS.md‎

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| `packages/acp-server` | Agent Client Protocol host over engine v2 | Drives the engine through a `klient` memory-transport facade. |
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| `packages/pi-tui` | Vendored TUI library | Upstream fork with local divergences; tests run with `node --test`, not vitest. See its `AGENTS.md`. |
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| `packages/protocol` | Shared REST + WS protocol schemas | Envelope, error codes, pagination, WS-control types. |
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| `packages/remote-control` | Remote Control tunnel client | Registers this machine with a relay and forwards HTTP/WebSocket traffic to the local server, behind a machine-wide single-instance lock. Consumed by agent-gateway (the `/api/v1/remote-control` toggle) and the CLI (`pythinker web --remote-control`). |
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The web bundle: `apps/pythinker-code/dist-web` is the committed, prebuilt bundle of `apps/pythinker-web` (built with `pnpm --filter @pymodel/pythinker-web run build` and copied via `scripts/copy-web-assets.mjs`). `apps/pythinker-code/scripts/check-web-assets.mjs` fails when the bundle is missing **or stale** (it compares a fingerprint of every `apps/pythinker-web` build input against the one recorded at copy time); it runs in pre-push, in the CLI `build`, and on `prepack`. Whenever you touch the web UI, run `pnpm run build:web` and commit the restaged bundle in the same change. `packages/server` and `packages/server-e2e` are empty leftover directories excluded from the workspace — not packages.
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‎apps/desktop/scripts/finalize-mac-artifacts.ts‎

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.sort()
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if (dmgs.length === 0) throw new Error(`No DMG artifacts found in ${options.distDir}`)
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const manifestName = options.manifestName ?? DEFAULT_MAC_MANIFEST
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// The workflow always passes the channel manifest positionally, so an unresolved
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// channel output arrives as an empty string rather than a missing argument; `??`
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// would keep it and read the distribution directory itself.
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const manifestName =
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options.manifestName === undefined || options.manifestName === ''
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? DEFAULT_MAC_MANIFEST
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: options.manifestName
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const metadataPath = join(options.distDir, manifestName)
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let metadata = readFileSync(metadataPath, 'utf8')
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const credentialArgs = buildNotarytoolArguments(options.env)

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