Three-part fix for the false "unknown config key(s)" warning fired for
top-level `branching_strategy` in .planning/config.json:
1. On-disk migration (option 3, mirroring multiRepo → planning.sub_repos):
When loadConfig reads a config.json with top-level `branching_strategy`
set and `git.branching_strategy` unset, it grafts the value into
`git.branching_strategy` and deletes the top-level key, then persists.
If `git.branching_strategy` is already set, the nested value wins
(matches SDK mergeDefaults precedence, PR #3116).
2. KNOWN_TOP_LEVEL safety net: 'branching_strategy' added to the deprecated-
keys bucket so the warning never fires even on the first read of a root
config that feeds a workstream merge (where `parsed` may still carry it).
3. Double-emission guard: a module-level `_warnedUnknownConfigKeys` Set
deduplicates the unknown-key warning across multiple loadConfig calls
within a single CLI invocation (init phase-op N called it twice).
Closes#3523
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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