fix(install): harden ECC installer lifecycle

Make Antigravity 2.0 installs native and safely migrate legacy state. Ensure doctor, repair, status projection, repeat installs, legacy Codex sync, and uninstall converge without losing user files. Exclude Python bytecode and harden repo-scan bootstrap guidance.

Gate publishing and pull-request merges on one exact packed artifact completing install, repeat, drift, repair, status, and uninstall across Linux, macOS, and Windows.

Co-authored-by: lorencifernando-coder <lorenci.fernando@gmail.com>

Co-authored-by: Suliman Abdulrazzaq <suliman9000a@gmail.com>

Co-authored-by: Wu Shuwen <mikewushuwen@outlook.com>

.codex-plugin/README.md

@@ -79,13 +79,19 @@ not create a second scope or duplicate hook registration.
 
 ## Native plugin versus legacy managed sync
 
-The commands above are the native Codex plugin path. The legacy managed sync
+The commands above are the native Codex plugin path. The deprecated legacy managed sync
 (`bash scripts/sync-ecc-to-codex.sh`) is a separate compatibility
 path that merges files into `~/.codex`. It is not a native plugin install and
 does not create a marketplace registration. Prefer the native path on current
 Codex; use the legacy managed sync only when you intentionally need its copied
 configuration layer.
 
+New sync runs record a versioned ownership manifest. Inspect or remove that
+layer explicitly with `ecc uninstall --legacy-codex-sync --dry-run`, followed
+by `ecc uninstall --legacy-codex-sync`. Cleanup never targets conversation
+history or native plugin caches. Older pre-manifest installs are cleaned
+conservatively and unverifiable files are retained with warnings.
+
 After install, `codex plugin list` is only a registration check. From an ECC
 checkout, run the cache check to verify that the installed manifest can resolve
 its referenced skills, MCP config, and assets: