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The superseded personal-config Agent Note and its superseding profile note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.

apps/cli/tests/fixtures/invalid-provider.cordis.yml

@@ -1,4 +1,4 @@
-# Invalid raw overlay used to prove boot failures settle and exit.
+# Invalid `--patch` overlay used to prove boot failures settle and exit.
 
 - id: llm-pi-ai
   config:

apps/cli/tests/fixtures/raw-overlay.cordis.yml

@@ -1,12 +0,0 @@
-# Raw CLI overlay used by the built config-dump acceptance test.
-
-- id: agent-loop
-  config:
-    agents:
-      - id: configured
-        provider: configured-provider
-        model: configured-model
-
-- id: absent-row
-  config:
-    value: unmatched