cmdInitManager called fs.readdirSync(phasesDir) and compiled a new
RegExp inside the per-phase while loop. At 50 phases this produced
50 redundant directory scans and 50 regex compilations with full
ROADMAP content scans.
Move the directory listing before the loop and pre-extract all
checkbox states via a single matchAll pass. This reduces both
patterns from O(N^2) to O(N).
Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>