fix: reconcile sub-directory AGENTS.md in managed_section mode and never write into nested Git worktrees (#2560)

[Aryan Singh K. (aryansk)]

Closes #2560

Summary

Fixes two silent data-loss bugs in the distributed AGENTS.md write path, exactly as the triage panel's suggested action describes.

Case A — sub-directory AGENTS.md loses hand-authored content under managed_section

_prepare_distributed_file scoped managed-section reconciliation to the root AGENTS.md only (the is_root guard added in #1764). A sub-directory file carrying the markers was overwritten whole, destroying content outside the managed block even though the user had opted into managed_section.

Fix: drop the is_root guard. Marker presence now decides at any depth; a file without markers raises ManagedSectionError instead of being silently replaced (the existing conservative behavior).

Case B — writes into nested independent Git repositories

The write path never checked Git boundaries, so a placement whose parent directory is the root of a nested worktree (a .git file, not directory) was written into a repository APM was never pointed at — leaving an uncommitted modification in a foreign repo.

Fix: mirror the orphan-sweep boundary check (distributed_compiler.py) on the write path: skip the placement with a warning.

Changes

• src/apm_cli/compilation/agents_compiler.py: drop the is_root guard from the managed_section branch; add _is_nested_git_worktree() and apply it in both the batch write loop and _write_distributed_file.
• tests/unit/compilation/test_managed_section.py: the old "subdir ignores managed_section" test now asserts marker reconciliation (the [BUG] Sub-directory AGENTS.md is overwritten whole, ignoring managed_section and foreign Git roots #2560 regression); added a nested-Git-worktree skip test.

Validation

• pytest tests/unit → 19,803 passed, 2 skipped, 21 xfailed
• ruff check + ruff format clean

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