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.

apps/cli/src/app-cli-entry.ts

@@ -4,9 +4,9 @@
  * Everything here is what must exist before the Loader runs: the patch
  * composition over the shipped base and surface overlay (CLI flags + the
  * resolved frontend dist), and the fail-loud activation audit after the tree
- * settles. The environment is what the bin already loaded (ambient plus the
- * invoking directory's `.env`); `$DSH_HOME/.env` belongs to the credential
- * provider and is never hoisted here.
+ * settles. The environment is what the bin already loaded (ambient over the
+ * invoking directory's `.env` over `$DSH_HOME/.env`); credentials live in
+ * `$DSH_HOME/.credentials.yaml` and are never hoisted into it.
  */
 
 import { readFileSync } from 'node:fs'

apps/cli/src/bin.ts

@@ -10,7 +10,7 @@
 
 import { readFileSync } from 'node:fs'
 import { fileURLToPath } from 'node:url'
-import { loadEnv } from '@deepseek-ai/dsh-app-boot'
+import { loadLayeredEnv } from '@deepseek-ai/dsh-app-boot'
 import { parseDshArgs } from './args.ts'
 
 // Both the source tree (apps/cli/src) and the bundled bin (apps/cli/lib) sit
@@ -24,7 +24,7 @@ function readVersion(): string {
   return typeof manifest.version === 'string' ? manifest.version : '0.0.0'
 }
 
-loadEnv('dsh')
+loadLayeredEnv('dsh')
 // The env opt-in is read at the process boundary; `1` is the documented value.
 const invocation = parseDshArgs(process.argv.slice(2), readVersion(), process.env.DSH_EXPERIMENTAL === '1')
 

apps/cli/src/tui.ts

@@ -115,12 +115,11 @@ export async function runTui(
     )
     process.exit(1)
   }
-  // The bin already loaded the invoking directory's .env, and that is the
-  // whole environment: $DSH_HOME/.env is credentials-local's writable store,
-  // and hoisting it would make every stored key read as a read-only ambient
-  // override on the next run — unrotatable from the TUI or the web page.
-  // The environment is settled, so switching the workspace here cannot alter
-  // its precedence. The cwd IS the workspace seam: the shipped config
+  // The bin already loaded both environment files, and that is the whole
+  // environment: credentials live in `$DSH_HOME/.credentials.yaml`, which is
+  // never hoisted, so a stored key stays rotatable from the TUI and the web
+  // page. The environment is settled, so switching the workspace here cannot
+  // alter its precedence — the project layer is the *invoking* directory's. The cwd IS the workspace seam: the shipped config
   // resolves the session cwd and the HMR watch root from it, so one chdir moves
   // both together. Sessions themselves live under the Harness home so `/resume`
   // spans every workspace, and are unaffected by this chdir.