initProgress computed phase status purely from disk (PLAN/SUMMARY counts),
consulting the ROADMAP `- [x] Phase N` checkbox only for phases with no
directory. initManager, by contrast, applied an explicit override: a
ROADMAP `[x]` forces status to `complete` regardless of disk state.
Result: a phase with a stub directory (no SUMMARY.md) and a ticked
ROADMAP checkbox reported `complete` from /gsd-manager and `pending`
from /gsd-progress — same data, different answer.
Apply ROADMAP-[x]-wins as the unified policy inside initProgress, mirroring
initManager's override. A user who typed `- [x] Phase 3` has made an
explicit assertion; a leftover stub dir is the weaker signal.
Adds sdk/src/query/init-progress-precedence.test.ts covering six cases
(stub dir + [x], full dir + [x], full dir + [ ], stub dir + [ ],
ROADMAP-only + [x], and completed_count parity). Pre-fix: cases 1 and 6
failed. Post-fix: all six pass. No existing tests were modified.
Closes#2674
b1278f6fc3