fix: retire leftovers of the removed $DSH_HOME/config.yaml personal overlay

The profile rework left references to the old entry modes behind. Renames
the user patch-layer API and its spec file (watchPersonalPatches ->
watchUserPatches, personal-config.spec.ts -> user-patches.spec.ts) and
retargets the prose that still named `config.yaml`, `--config`, raw-config
mode, and surface overlays: repository-plugin and mcp-memory READMEs, the
credentials-local anchor into app-boot, vendor manifest items 12-13, the
vendored include/hmr comments, and install.sh.

Restores the boot-failure guard the rework dropped with raw mode: the
built-bin case now boots `--profile web --patch <invalid>` and asserts the
settled diagnostic and exit 1, so the HMR initial-scan deadlock stays
covered; its orphaned raw fixture is renamed and the unused one deleted.
The superseded personal-config Agent Note and its superseding profile note
are now cross-linked.

vendor/hmr/src/index.ts

@@ -215,7 +215,7 @@ class Hmr extends Service {
       // the scan-triggered refresh waits on that apply — a teardown deadlock
       // that strands boot without a diagnostic. Only events after the scan
       // matter here; `registerConfig` keeps its own initial scan because a
-      // personal config present at registration must apply once.
+      // user patch layer present at registration must apply once.
       ignoreInitial: true,
     })