refactor(cli)!: one shared base config with per-surface overlays

`dsh` shipped two config trees that were 43 rows the same: apps/cli/cordis.yml
composed web as 74 flat rows, while the TUI booted examples/tui-agent/cordis.yml
whose single `@deepseek-ai/dsh-tui-demo` row mounted twelve plugins behind a
twenty-key pass-through Config. Neither file was what its location claimed —
apps/cli hardcoded the "example" as the product default and the "demo" bundle
was the application — and every capability change had to be made twice.

- apps/cli/base.cordis.yml holds the 43 shared rows; tui.cordis.yml and
  web.cordis.yml are patch lists stating only what differs per surface
- overlays apply as SIBLING patch lists at one include level, because include
  patches never cross an include boundary. Precedence: base < surface <
  (--config | personal ~/.dsh/config.yaml) < launcher flag/profile patches
- `--config` now applies an overlay INSTEAD OF the personal one, so a demo or
  test tree never inherits the user's route; new `--config-replace` boots a file
  as the entire tree (the old `--config` behaviour). Both survive /resume
- vendor/include: index each `insert`ed row as it is added so a later patch can
  configure or disable it. Upstream built the id index once before the patch
  loop, leaving every surface-only row — the whole TUI front door — silently
  unpatchable from user config. Logged as local modification 8
- session identity moves to dsh-agent-loop's CONFIGURED_AGENT_IDENTITIES_KEY;
  dsh-tui's MAIN_SESSION_ID_KEY is deleted (only the bundle read it)
- delete examples/tui-agent, examples/cordis-agent, packages/examples/tui-demo;
  TUI tests → apps/cli/tests, cordis e2e → packages/cordis/tool-cordis/tests,
  examples/code-mode survives as an overlay leaf
- `dsh web` gains --config, threaded into AppCLIEntry as an extra overlay

Three latent defects surfaced and are fixed here: the TUI captured the optional
sessionQuery service once at construction and could permanently disable /resume
when it won the mount race; the session-store root silently reverted to a
project-local ./.sessions; --config-replace was dropped by the resume handoff.

Verified by booting each tree through the real Loader (TUI 55 entries, web 75,
zero unsettled) rather than reading YAML. All eight terminal snapshots replay
byte-identically; 14/14 PTY smoke, 112/112 snapshots, 25/25 doc-sync, hygiene
and lint clean.

vendor/README.md

@@ -37,7 +37,7 @@ Keep this log exhaustive — every divergence from upstream must be listed.
 5. **`schemastery/tsdown.config.ts` and `logger-console/tsdown.config.ts`**: ours, not upstream files — per-package build-shape overrides (dual ESM+CJS output; separate node/browser entries) for the repo-root tsdown build. They read the JS emitted under `lib/types` and then write the publish runtime entries under `lib/`. Like the regenerated tsconfigs, they are not part of the upstream sync surface.
 6. **`cordis/src/fiber.ts` lifecycle hardening**: locally closes three reentrant disposal gaps. An effect's owner-list wrapper is registered before its setup body runs, so an unload begun from inside setup awaits setup and every collected cleanup; synchronous setup failure removes the wrapper and rolls back collected cleanup. Async cleanup stays owner-visible until quiescence, and Cordis's internal effect composition joins an already-running cleanup while repeated public disposer calls retain their upstream single-shot result. Effect creation is rejected while the owner is `UNLOADING` (while `PENDING` and `LOADING` remain legal), preventing cleanup-time registrations from escaping the unload snapshot. Child fibers register and receive their parent-owned disposer before `internal/plugin` publication, resolve dependency declarations added by that notification before activation, drain effects attached while pending, skip plugin execution when reentrant disposal invalidates the load epoch before its first checkpoint, and contain teardown-notification failures per observer so one callback cannot starve peers or interrupt ownership cleanup.
 7. **`cordis/src/*.ts` JSDoc enrichment**: added `@param`/`@returns` tags and contract documentation (disposal semantics, waterfall veto, bail conditions, error cases) across the public plugin-author surface — `Context` (class, statics, and the `Context` interface properties incl. `root`), `EventsService`, `Fiber`, `RegistryService`, `ReflectService`, `Service`, `LoggerService` and their `declare module './context.ts'` overloads. Comment-only; no code changes. Motivation: the website API-reference generator renders these docs and hard-errors on undocumented members. Retire this entry when the enrichment is upstreamed to the fork.
-8. **`include/src/index.ts` hot-reload hardening**: `refresh()` awaits the full read-and-update and catches failures (logging a warning and keeping the last good entry tree) instead of rethrowing — upstream's throw escaped `@cordisjs/plugin-hmr`'s async watcher callback as an unhandled rejection, so one bad `cordis.yml` edit killed a live app. `read()` rejects a non-array parse result (an empty or mid-write truncated file parses to `undefined`, which upstream later crashed on) and commits `content`/`data` only on success, so reverting an edit to the exact last good content reads as "unchanged". `refresh()` and the `internal/update` listener re-apply `config.patches` before `root.update()`, matching initial load; upstream applied patches only in `[Service.init]`, so any config hot-reload silently reverted overlay-patched entries and removed inserted ones. `applyPatches` deep-copies via `structuredClone` instead of mutating the cached parse (repeated application converges; removing a patch reverts), and the veto-style `internal/update` listener persists the incoming config itself (`Fiber.update` only assigns behind `next()`), so later re-reads use the new patches. `[Service.init]` falls back to `initial` only on `ENOENT`; an existing-but-invalid file fails loud with its real parse error instead of "config file not found" (or a silent overwrite). Covered by `packages/ui/app-boot/tests/config-reload.spec.ts`.
+8. **`include/src/index.ts` hot-reload hardening**: `refresh()` awaits the full read-and-update and catches failures (logging a warning and keeping the last good entry tree) instead of rethrowing — upstream's throw escaped `@cordisjs/plugin-hmr`'s async watcher callback as an unhandled rejection, so one bad `cordis.yml` edit killed a live app. `read()` rejects a non-array parse result (an empty or mid-write truncated file parses to `undefined`, which upstream later crashed on) and commits `content`/`data` only on success, so reverting an edit to the exact last good content reads as "unchanged". `refresh()` and the `internal/update` listener re-apply `config.patches` before `root.update()`, matching initial load; upstream applied patches only in `[Service.init]`, so any config hot-reload silently reverted overlay-patched entries and removed inserted ones. `applyPatches` deep-copies via `structuredClone` instead of mutating the cached parse (repeated application converges; removing a patch reverts), and the veto-style `internal/update` listener persists the incoming config itself (`Fiber.update` only assigns behind `next()`), so later re-reads use the new patches. `[Service.init]` falls back to `initial` only on `ENOENT`; an existing-but-invalid file fails loud with its real parse error instead of "config file not found" (or a silent overwrite). `applyPatches` also indexes each `insert`ed entry as it is added, so a later patch in the same list can configure or disable a row an earlier patch inserted; upstream built the id index once before the patch loop, leaving inserted rows silently unpatchable. That matters because `dsh` composes one shared base (`apps/cli/base.cordis.yml`) with a surface overlay, an optional `--config` overlay, and the personal `~/.dsh/config.yaml` as sibling patch lists at one include level — patches never cross an include boundary, so surface-only rows would otherwise be unreachable from user config. Covered by `packages/ui/app-boot/tests/config-reload.spec.ts`.
 9. **Vendored Node-compatible TypeScript**: marked erased imports explicitly across `cordis`, `loader`, `include`, `hmr`, and `schemastery` so Node's native TypeScript transform does not request types as runtime exports. Schemastery's source uses an ESM default export and its package declares `type: module`; its built ESM/CJS entries retain explicit `.mjs`/`.cjs` extensions.
 
 ## Sync procedure

vendor/include/src/index.ts

@@ -163,6 +163,12 @@ export class Include extends EntryTree {
         } else {
           data.push(...insert)
         }
+        // Index what this patch added so a LATER patch in the same list can
+        // target it. Patch lists compose one layer per source (surface overlay,
+        // then `--config`, then the user's), and a layer must be able to
+        // configure or disable a row an earlier layer inserted; without this,
+        // inserted rows were silently unpatchable.
+        buildMap(insert)
         continue
       }