Upgrade the Atomic harness to 0.9.29

@bastani/atomic, @bastani/atomic-natives and @bastani/pi-ai move to
0.9.29. Atomic's @earendil-works packages stay at 1.1.0, and no other
lockfile entry changes. The five builtin packages are unchanged, so
BUILTINS_OFF still turns off each one for the isolated Planner.

Assistant-workflow: inline
Assistant-model: Claude Opus 5.5 (fast)
Assistant-duration: 4m converged, estimated 20m
Assistant-verification: bun test passed: 4407 pass, 3 skips, 0 fail, with GIT_CONFIG_GLOBAL=/dev/null
Assistant-verification: bun run types passed: all workspace checks
Assistant-verification: bun run ci passed: dprint, oxlint, tokens, design contract, design record, Impeccable (no new findings)
Assistant-verification: source check passed: Atomic 0.9.29 dist/builtin lists intercom, mcp, subagents, web-access, workflows
User-preference: Keep pdd-kit and Chopin on the same Atomic release, with transitive deps upgraded together
Co-authored-by: Alex Lavaee <lavaman131@github.com>