warn: Claude plugin manifest exists and is not managed by dotagents

[dakshshah96]

Environment

• @sentry/dotagents version 3.1.0
• macOS
• Project-scoped installation targeting Claude and Codex
• Command: npx -y @sentry/dotagents@3.1.0 --project install

Steps to Reproduce

1. Configure plugins that ship both .claude-plugin/plugin.json and .codex-plugin/plugin.json, without a root plugin.json:

   agents = ["claude", "codex"]
   
   [[plugins]]
   name = "posthog"
   source = "PostHog/ai-plugin"
   path = "."
   targets = ["claude", "codex"]
   
   [[plugins]]
   name = "pstack"
   source = "michael-denyer/pstack-claude"
   path = "plugins/pstack"
   targets = ["claude", "codex"]

2. Run:

   npx -y @sentry/dotagents@3.1.0 --project install

3. Run the command again. The same warnings recur.

This also reproduces with a minimal local plugin containing only these two files:

source/
├── .claude-plugin/plugin.json
└── .codex-plugin/plugin.json

Each file can contain:

{
  "name": "dual-native",
  "version": "1.0.0"
}

Declare the local plugin with:

agents = ["claude", "codex"]

[[plugins]]
name = "dual-native"
source = "path:./source"
targets = ["claude", "codex"]

Expected Result

Dotagents recognizes both manifests as publisher-authored files belonging to the installed plugin, preserves their runtime-specific content, and emits no unmanaged-manifest warnings.

This should remain true after reinstalling or reloading installed state.

Actual Result

Every install emits:

warn: Claude plugin manifest exists and is not managed by dotagents: <repo>/.agents/plugins/posthog/.claude-plugin/plugin.json
warn: Claude plugin manifest exists and is not managed by dotagents: <repo>/.agents/plugins/pstack/.claude-plugin/plugin.json

The Claude manifests remain intact, but dotagents incorrectly treats files it copied from the plugin source as unrecognized files.

Source inspection suggests the following cause:

• loadPluginInterfaces() checks native fallback manifests in Codex-first order.
• It returns after the first match and registers only that runtime in authoredNativeInterfaces.
• Installation copies both native manifests, but .dotagents-native-source and .dotagents-native-fallbacks record only codex.
• writePluginManifests() encounters the Claude manifest without authored provenance or a managed-file marker, then warns and skips it.

A fix likely needs to discover and preserve all publisher-authored native interfaces. The installed-provenance validation also currently rejects multiple fallback runtimes when nativeSource is set, so that invariant would need updating.

Verified with a minimal reproduction across fresh installation, repeated installation, and installed-state reload.