fix(backup): don't stage targets for skipped missing-source items

[k9ert]

Problem

argit backup aborts with:

git add failed: fatal: pathspec 'hermes/data/scripts/' did not match any files

_git_commit staged it.target for every non-secret manifest item, including items whose source was absent on the agent and therefore skipped during the copy phase (§4–7). The destination was never written, so git add failed and took down the whole backup.

This triggers whenever the running agent lacks a path the bundled manifest declares — e.g. the hermes-2026.5.4-1 manifest declares scripts/, whatsapp/, memory_store.db, workspace/, but a 2026.5.7 Hermes build doesn't create them. Found while wiring argit into Hermes provisioning (bot-provisioning-poc#12) — the systemd backup unit failed on first run and left a .argit/in-progress marker that blocked every retry.

Fix

Stage only targets that actually exist on disk after the copy phase:

if it.target and (repo_root / it.target).exists():
    paths_to_add.append(it.target)

General and version-agnostic — a manifest will never perfectly match every Hermes patch release, so backup should tolerate declared-but-absent paths (it already logs and skips them during copy; this aligns staging with that).

Test

Adds test_git_commit_skips_items_with_missing_target to tests/unit/test_backup_review_staging.py — a present-target item is staged, a missing-target item is not. Full unit suite green.

🤖 Generated with Claude Code

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