Upgrade the Atomic harness to 0.9.25

0.9.25 is the stable release that rolls up the 0.9.25 prereleases,
including SDK workflow run control and the native MCP client. It ships
the same five builtin packages, so BUILTINS_OFF still turns off each one
for the isolated Planner.

Assistant-model: Claude Opus 5.5
Assistant-workflow: inline
Assistant-verification: bun test passed: 1824 pass, 2 PostgreSQL skips, 0 fail
Assistant-verification: bun run types passed: all workspaces
Assistant-verification: bun run ci passed: dprint, oxlint, tokens, design contract, design record, Impeccable (no new findings)
Assistant-verification: source check passed: @bastani/atomic 0.9.25 dist/builtin lists intercom, mcp, subagents, web-access, workflows
Co-authored-by: Alex Lavaee <lavaman131@github.com>