Dolt/beads reliability: journal corruption prevention, port pinning, boundary scan fixes

[alexsiri7]

Fix several Dolt and beads reliability issues:

• Prevent Dolt journal corruption on server shutdown (graceful flush)
• Pin BEADS_DOLT_PORT and BEADS_DIR to prevent cross-rig routing failures
• Set cwd to data_dir when launching dolt sql-server
• Exclude worktrees/ from bd boundary scan to prevent false positives
• Correct greedy sed in health.sh dolt_database extraction
• Use valid bead type 'chore' for nudge beads instead of invalid 'nudge'

These fix data corruption and cross-rig contamination issues in multi-rig deployments with shared Dolt servers.