set_nspawn_flags propagated has_cap's error, so one corrupt
capabilities.json failed every agent's Start, spawn and Swap. It now
goes through holds_manage_root_agent, which logs the error (agent and
file) and treats the capability as absent: the agent starts without the
cross-agent, /applied and /meta mounts. caps_for/has_cap take the file
path so that seam is testable against a tempfile.
- meta.rs: a comment at the render_flake reads records why they
propagate (an empty tool-groups map renders toolGroups = null, i.e.
AGENT_DEFAULT, which fails open for narrower explicit entries).
- capabilities::read doc: states when set_caps/remove_agent rewrite
the file instead of saying remove_agent repairs it.
- set/remove corrupt-file tests assert ErrorKind::InvalidData.
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