[BUG] APM 0.33.0: apm update fails to integrate Azure Skills because frozen hook metadata is not JSON serializable #3167

With APM CLI 0.33.0, apm update fails while integrating microsoft/azure-skills:

[x] 1 package failed:
    +- microsoft/azure-skills -- Failed to integrate primitives: Object of type mappingproxy is not JSON serializable
[x] Installation failed with 1 error(s). 

Environment

• APM CLI: 0.33.0
• Reported installation: Windows, WinGet standalone executable and macOS 27.01 (Homebrew)
• Dependency: microsoft/azure-skills
• Targets: claude, codex, copilot

Steps to reproduce

Use APM CLI 0.33.0.
Add microsoft/azure-skills to an APM project with the following configuration.
Run apm update.

name: apm-hook-repro
version: 1.0.0
description: Minimal Azure Skills integration reproduction
author: APM user
targets:
  - claude
  - codex
  - copilot
dependencies:
  apm:
    - microsoft/azure-skills

The dependency is not pinned here; reproduction depends on it containing hooks with nested metadata, such as an env object.

Expected behavior

APM integrates the hooks successfully, preserving their environment variables
and other metadata in the generated native JSON documents.

Actual behavior

Integration fails with the error above, and the install transaction is not committed.

Root cause

src/apm_cli/hook_contract.py recursively freezes hook metadata in _freeze:
dictionaries become MappingProxyType instances, and lists become tuples.
This is appropriate for the immutable intermediate representation (IR).

However, src/apm_cli/integration/hook_native_formats.py only makes a shallow
copy with dict(handler.metadata) and dict(binding.metadata). Nested mappings
remain frozen. The raw-entry paths also return frozen metadata directly.
Consequently, JSON serialization fails when it encounters a nested mapping proxy.

The failure can be reproduced without downloading Azure Skills or executing hooks:

import json
from apm_cli.integration.hook_native_formats import _to_claude_hook_entries

entries = [{
    "bash": "echo test",
    "env": {"APM_TEST": "value"},
}]
json.dumps(_to_claude_hook_entries(entries))

Proposed fix

Recursively materialize metadata at the native rendering boundary:

• Convert Mapping values to new dictionaries.
• Convert lists and tuples to new lists, recursively converting their elements.
• Preserve scalar values.
• Apply the conversion to handler metadata, binding metadata, and raw entries in
  both the nested and flat rendering paths.

Keep the IR immutable. Do not stringify unsupported values with default=str,
discard env, or change dependency declarations as a workaround.

Regression coverage

• JSON round trips for Claude, Codex, Gemini, and nested/flat Antigravity adapters.
• Preservation of nested env, extension metadata, arrays, and scalar values.
• Preservation of commands, timeout conversion, matchers, and provenance.
• Raw-entry round trips, including mappings inside arrays.
• Mutation of rendered output does not mutate the source or frozen IR.
• Gemini's in-place compatibility conversion preserves env.