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The superseded personal-config Agent Note and its superseding profile note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/include/src/index.ts

@@ -85,10 +85,10 @@ export function applyEntryPatches(
         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.
+      // target it. Patch lists compose one layer per source (each bundle
+      // layer, then the user's, then `--patch` overlays), 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
     }