Docs: link the obvious orphan docs + resolve connect-to-server spec; handle paren dirs in docs-reachable

Connected 17 of the 23 orphaned docs to the reachable tree (230 → 247 reachable, 6 orphans left, all deliberately deferred):

- **`connect-to-server-plan.md`**: investigation confirmed it shipped in v0.11.0 (manual SMB "Connect to server", `network/manual_servers.rs` + MCP tools + dialog). Moved out of `later/` to the specs root and ticked in the index.
- **4 subsystem dirs** named in `architecture.md` / `apps/desktop/CLAUDE.md` so their CLAUDE.md resolve (`routes/(main)/`, `apps/desktop/scripts/`, `packaging/homebrew/`).
- **Guides** linked from their natural homes: the three dependency guides from `architecture.md` § Dependency management; signing + homebrew-cask from `releasing.md`; benchmarking/error-handling/mcp-development from the colocated `listing` / `friendly_error` / `mcp` CLAUDE.md; generating-test-files from `tooling/testing.md`; multi-agent-refactors from `AGENTS.md` § Workflow.
- **Notes** linked from the subsystem they inform (`smb-auth-flow-redesign` → network, `sort-order-shortcut-research` → shortcuts) and `notes/README.md` from `AGENTS.md`.

Also: `docs-reachable` now resolves SvelteKit group dirs (parens in backtick directory references), so `routes/(main)/` connects. Parens stay out of the file-token regex (they'd swallow a `](path)` delimiter); a test covers the dir case.

Left as orphans for us to decide (stale / no code home): `benchmarks/smb/CLAUDE.md`, `guides/test-purchase-flow.md`, `guides/testing/index.md`, `guides/testing/setting-up-smb-test-containers-on-linux.md`, `notes/disk-cleanup-advice-process.md`, `notes/totalcmd-plugin-analysis.md`.

Author: vdavid

AGENTS.md

@@ -107,7 +107,8 @@ Core structure:
 - `/brand/` - Tracked brand/press-kit assets (logos, master screenshots, marketing copy). See its `CLAUDE.md`
 - `/docs/` - Dev docs
   - `guides/` - How-to guides
-  - `notes/` - Temporary reference notes (benchmarks, analysis) linked from CLAUDE.md files
+  - `notes/` - Temporary reference notes (benchmarks, analysis) linked from CLAUDE.md files; see
+    [notes/README.md](docs/notes/README.md)
   - `specs/` - Per-development specs and task lists (temporary, periodically wiped); see
     [specs/index.md](docs/specs/index.md)
   - `tooling/` - Internal tooling docs
@@ -296,6 +297,7 @@ shims on PATH; if `go` / `node` isn't found, check that `~/.local/share/mise/shi
 - **Don't `git push` without explicit approval, and don't push routinely** (solo work, limited CI). See the
   `push-cadence` and `no-external-actions` user rules.
 - Step back and reflect per milestone. Is what you did solid AND elegant? Are you confident AND proud?
+- For large parallel-agent efforts, see [multi-agent refactors](docs/guides/multi-agent-refactors.md).
 - **The delivery pipeline is fully wired; don't re-audit it.** Releases are agent-automated end to end (tag → CI
   build/sign/notarize → publish `latest.json` → website deploy → silent in-app update via the FDA-preserving updater),
   and user-feedback loops are live (crash reports → email cron, error reports → instant Discord webhook, anonymous

apps/desktop/CLAUDE.md

@@ -50,6 +50,7 @@ Don't delete either shield. If a new always-edited non-build file type shows up
 
 - `src/`: Svelte frontend (SvelteKit static adapter, TypeScript strict, custom CSS with design tokens)
 - `src-tauri/`: Rust backend (Tauri 2, serde, notify, tokio)
+- `scripts/`: dev/build scripts (the `scripts/tauri-wrapper.js` wrapper, instance-isolation); see its `CLAUDE.md`
 - `scripts/tauri-wrapper.js`: dev/build wrapper (env vars, dev config injection)
 - `test/`: Vitest unit tests
 - `test/e2e-linux/`: WebDriverIO + tauri-driver E2E tests (Docker)

apps/desktop/src-tauri/src/file_system/listing/CLAUDE.md

@@ -2,6 +2,8 @@
 
 Backend directory reading, caching, sorting, and streaming for the file explorer. Handles 100k+ file directories with non-blocking I/O and progress events.
 
+For profiling listing performance, see `docs/guides/benchmarking-file-loading.md`.
+
 ## Architecture
 
 ### Module structure

apps/desktop/src-tauri/src/file_system/volume/friendly_error/CLAUDE.md

@@ -8,6 +8,8 @@ we show a friendly title, a plain-language explanation, and provider-specific ad
 Parent: [`volume/CLAUDE.md`](../CLAUDE.md). The trait + manager + capability matrix live there; this file is just the
 error-mapping subsystem.
 
+For the broader error-handling conventions across the app, see `docs/guides/error-handling.md`.
+
 ## Philosophy
 
 **The user should never feel alone with a broken state.** Every error message should feel like the app is putting its

apps/desktop/src-tauri/src/mcp/CLAUDE.md

@@ -3,6 +3,8 @@
 Exposes Cmdr to AI agents via the Model Context Protocol. Security model is parity: agents can only do what users can
 do, no filesystem access. Streamable HTTP transport, `127.0.0.1` only, ephemeral port by default.
 
+For adding or changing tools, see `docs/guides/mcp-development.md`.
+
 ## Module map
 
 - `server.rs`: HTTP server, bind/lifecycle, auth gate (`tool_call_requires_token`, `validate_token`, `validate_origin`).

apps/desktop/src-tauri/src/network/CLAUDE.md

@@ -5,6 +5,8 @@ Discover, browse, and mount SMB network shares on macOS and Linux. Discovery via
 
 Frontend counterpart: [`apps/desktop/src/lib/file-explorer/network/CLAUDE.md`](../../../src/lib/file-explorer/network/CLAUDE.md).
 
+Background on the auth flow design: `docs/notes/smb-auth-flow-redesign.md`.
+
 ## Module map
 
 - Discovery + servers: `mdns_discovery.rs`, `manual_servers.rs`, `virtual_smb_hosts.rs` (E2E, `smb-e2e` feature only).

apps/desktop/src/lib/shortcuts/CLAUDE.md

@@ -3,6 +3,8 @@
 Customizable keyboard shortcuts for all Cmdr commands (edit/add/remove/reset via Settings or MCP). Defaults live in the
 sibling `../commands/command-registry.ts`; only customizations persist to `shortcuts.json`.
 
+Background on default sort-order shortcuts: `docs/notes/sort-order-shortcut-research.md`.
+
 ## Module map
 
 - `shortcuts-store.ts` (delta-only persistence, cross-window emit, the native/fixed boundary),

docs/architecture.md

@@ -64,6 +64,7 @@ All under `apps/desktop/src/lib/`.
 - `onboarding/`: Soft-sheet onboarding wizard: Full Disk Access, AI provider, open-beta analytics disclosure, optional
   settings
 - `ui/`: Shared UI primitives: ModalDialog, Button, AlertDialog, Notification, dialog registry, `SectionCard`
+- `routes/(main)/`: The main route: app orchestrator mounting the dual-pane explorer plus top-level dialogs
 - `routes/dev/components/`: Dev-only catalog of every `lib/ui/` primitive (Storybook replacement), in the Debug window
 - `tooltip/`: Lightweight tooltip primitive
 - `stores/`: App-wide reactive Svelte stores: volume list, restricted-paths state
@@ -153,6 +154,7 @@ All under `apps/desktop/src-tauri/src/`.
 - `apps/website/`: getcmdr.com marketing site (Astro + Tailwind v4), including the dev-only `/dev/blog` Markdown editor
   for drafting posts
 - `apps/website/public/hero/`: Hero illustration assets (frame + pane cutouts, dark/light)
+- `apps/desktop/packaging/homebrew/`: Homebrew cask shape source-of-truth and tap-bump flow
 - `scripts/check/`: Go unified check runner (~40 checks, parallel with dependency graph)
 
 ## Search
@@ -265,7 +267,9 @@ The check runner and E2E testing docs live colocated with their code:
 
 [Renovate](https://docs.renovatebot.com/) (`renovate.json` in repo root) auto-updates all dependencies (npm, Cargo, Go).
 Weekly grouped PRs for non-major updates (auto-merge), monthly for major (manual review). Security vulnerability patches
-get immediate auto-merging PRs regardless of schedule.
+get immediate auto-merging PRs regardless of schedule. For adding deps by hand, see
+[add an npm dependency](guides/add-npm-dependency.md), [add a Rust crate](guides/add-rust-dependency.md), and
+[update dependencies](guides/update-dependencies.md).
 
 ### External services
 

docs/guides/releasing.md

@@ -4,6 +4,9 @@ How to release a new version of Cmdr. An agent runs the whole flow via the `/rel
 monitors the build, verifies the public surface afterwards, and handles failure recovery. The human's role is to review
 the CHANGELOG draft, confirm the version, and click any macOS permission prompts.
 
+Related guides for the signing and distribution steps:
+[apple-signing-and-notarization.md](apple-signing-and-notarization.md) and [homebrew-cask.md](homebrew-cask.md).
+
 ## Prerequisites
 
 - `TAURI_SIGNING_PRIVATE_KEY` and `TAURI_SIGNING_PRIVATE_KEY_PASSWORD` in GitHub secrets