[BUG] Claude hook bundles drop nested package.json module metadata #2950

Describe the bug

When a Claude hook package places a JavaScript hook and its module metadata in a nested directory, APM deploys the JavaScript file but drops the nested package.json. APM then generates a CommonJS sidecar at the higher hook root, so Node executes the nested .js file with the wrong module semantics.

To Reproduce

Steps to reproduce the behavior:

1. Create a Claude hook package with this layout:

   hooks/
     hooks.json
     esm/
       entry.js
       package.json
   

2. Set hooks/hooks.json to:

   {
     "hooks": {
       "SessionStart": [
         {
           "hooks": [
             {
               "type": "command",
               "command": "node ./esm/entry.js"
             }
           ]
         }
       ]
     }
   }

3. Set hooks/esm/entry.js to an ES module, for example:

   import { writeFileSync } from "node:fs";
   writeFileSync(process.argv[2], "ok\\n");

4. Set hooks/esm/package.json to:

   { "type": "module" }

5. Install the package into a project with Claude hooks enabled by running apm install.

6. Inspect the deployed hook under .claude/hooks/<package>/hooks/esm/.

7. Observe that entry.js is present, but esm/package.json is missing. The generated .claude/hooks/<package>/hooks/package.json contains {"type": "commonjs"}.

8. Run the deployed hook with Node and observe an import syntax error because the file is treated as CommonJS.

Expected behavior

APM should preserve the nested hooks/esm/package.json, or generate equivalent module metadata at the deployed esm boundary. Running the deployed entry.js should use ES module semantics and complete successfully.

Environment (please complete the following information):

• OS: Windows
• Python Version: 3.12.13
• APM Version: 0.30.0

Logs

APM reports no installation error. Executing the deployed JavaScript file produces a Node module syntax error such as:

SyntaxError: Cannot use import statement outside a module

Additional context

src/apm_cli/integration/hook_bundle.py excludes every file named package.json in iter_deployable_hook_bundle_files, regardless of target. Claude passes exclude_json_files=False, but that option only controls the broader .json suffix filter and does not restore the skipped filename.

_hook_module_type searches the hook source root and its ancestors, not nested metadata directories. With no package-root or hooks/package.json, it therefore defaults to CommonJS and writes one sidecar at the deployed hook root.

This is distinct from #2824, which concerns missing .claude-plugin/plugin.json and other files outside the selected hook script bundle. This defect concerns module metadata inside an otherwise selected bundle.