Tom Boucher 06463860e4 fix(#2638): write sub_repos to canonical planning.sub_repos (#2668) ...

loadConfig's multiRepo migration and filesystem-sync writers targeted the
top-level parsed.sub_repos, but KNOWN_TOP_LEVEL (the unknown-key validator's
allowlist) only recognizes planning.sub_repos (canonical per #2561). Each
migration/sync therefore persisted a key the next loadConfig call warned was
unknown.

Redirect both writers to parsed.planning.sub_repos, ensuring parsed.planning
is initialized first. Also self-heal legacy/buggy installs by stripping any
stale top-level sub_repos on load, preserving its value as the
planning.sub_repos seed if that slot is empty.

Tests cover: (a) canonical planning.sub_repos emits no warning, (b) multiRepo
migration writes to planning.sub_repos with no top-level residue,
(c) filesystem sync relocates to planning.sub_repos, (d) stale top-level
sub_repos from older buggy installs is stripped on load.

Closes #2638

2026-04-24 18:05:33 -04:00

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