feat(credentials): move the store to .credentials.yaml and layer $DSH_HOME/.env

$DSH_HOME/.env carried two incompatible jobs. As credentials-local's writable
secret store it could not be hoisted into process.env — hoisting makes every
stored key read as a read-only launch override and blocks rotation from the
TUI and the web page. But its name and dotenv format promise an environment
file, so a DEEPSEEK_BASE_URL sitting beside a working DEEPSEEK_API_KEY in the
same file was silently ignored: only the credential provider read the
document, and it addresses credential references alone.

Split the two jobs into two files.

.credentials.yaml is the provider-managed store: a strict YAML mapping of
CredentialRef to non-empty string, no version field, no wrapper level. Because
it holds credentials and nothing else, a non-mapping root, a non-identifier
key, a non-string value, an empty string, a duplicate key, and malformed YAML
are all rejections rather than skipped entries — loud at boot and at a write,
warn-and-keep-last-good on a live reload. The dotenv physical-line editor
gives way to a patch of the parsed document, so comments and untouched entries
keep their formatting and any string value round-trips, multi-line included.
Writer lock, read-modify-write, atomic 0600 write under a 0700 directory,
watcher, self-write suppression, and quiescent disposal are unchanged.

$DSH_HOME/.env becomes the user's ordinary environment layer. app-boot's new
loadLayeredEnv loads the invoking directory's .env then the Harness home's,
giving user < project < inherited; the home resolves from the inherited
environment first, so a project .env cannot redirect it.

Credential precedence is unchanged: the live environment still wins read-only
over the file, and shadowed writes still reject. Whether a provider-managed
store should instead win over the environment is a separate decision.

No migration: a key already in $DSH_HOME/.env keeps resolving through the new
environment layer, as a read-only env source that shadows the stored one.

pnpm-lock.yaml

@@ -2625,12 +2625,12 @@ importers:
       chokidar:
         specifier: ^4.0.3
         version: 4.0.3
-      dotenv:
-        specifier: ^17.2.0
-        version: 17.4.2
       schemastery:
         specifier: ^3.18.0
         version: link:../../../vendor/schemastery
+      yaml:
+        specifier: ^2.9.0
+        version: 2.9.0
     devDependencies:
       '@deepseek-ai/dsh-atomic-write':
         specifier: workspace:^
@@ -9776,10 +9776,6 @@ packages:
   dompurify@3.4.11:
     resolution: {integrity: sha512-zhlUV12GsaRzMsf9q5M254YhA4+VuF0fG+QFqu6aYpoGlKtz+w8//jBcGVYBgQkR5GHjUomejY84AV+/uPbWdw==}
 
-  dotenv@17.4.2:
-    resolution: {integrity: sha512-nI4U3TottKAcAD9LLud4Cb7b2QztQMUEfHbvhTH09bqXTxnSie8WnjPALV/WMCrJZ6UV/qHJ6L03OqO3LcdYZw==}
-    engines: {node: '>=12'}
-
   dts-resolver@3.0.0:
     resolution: {integrity: sha512-1T1f+z+4tl9XD+m+0HBgWoL/nm0bOIffyWaUuUSBlFg/86IWvfx+wjNaO/ybU0AJzG9/Mi5hBUgGV6zCmWEN7Q==}
     engines: {node: ^22.18.0 || >=24.0.0}
@@ -14832,8 +14828,6 @@ snapshots:
     optionalDependencies:
       '@types/trusted-types': 2.0.7
 
-  dotenv@17.4.2: {}
-
   dts-resolver@3.0.0(oxc-resolver@11.20.0):
     optionalDependencies:
       oxc-resolver: 11.20.0