feat(ghidra): add atomic function annotation edits (#709)

* feat(ghidra): edit function annotations atomically

Return annotation readback and refreshed function analysis through CLI and MCP. Own each database transaction, invalidate caches and immutable snapshots, preserve executable bytes, and retain the Windows mutation boundary.

Assisted-by: Nitori (gensokyo-skills:nitori-reverse-engineering)

* fix(ghidra): preserve qualified function annotation identity

Preserve namespaces during local name writes and match qualified readback to the refreshed dossier. Add a producer-shaped regression and verify a real namespaced C++ function through the CLI.

Assisted-by: Nitori (gensokyo-skills:nitori-reverse-engineering)

* test(ghidra): align verification with annotation authority

Keep strict capability and profile checks while admitting the explicit session metadata operation. Verify packaged transport authority and atomic transaction commitments and preserve a read-only Windows expectation.

Assisted-by: Nitori (gensokyo-skills:nitori-reverse-engineering)

src/cliCommandNames.ts

@@ -14,6 +14,7 @@ export const CLI_COMMANDS = Object.freeze({
   capabilities: "capabilities",
   providers: "providers",
   function: "function",
+  annotateNativeFunction: "annotate-native-function",
   inspectNativeApi: "inspect-native-api",
   instructions: "instructions",
   search: "search",