Upgrade the Atomic harness to 0.9.25-alpha.2

SDK-created sessions now register workflows provided by packages their
resource loader resolves and keep package-contributed MCP servers
(bastani-inc/atomic#3372), so a full Planner in a checkout can run the
workflows that checkout installs. The release ships the same five builtin
packages, so the isolated workers' BUILTINS_OFF still covers each one.
Also applies dprint's formatting to the Planner workspace instructions.

Assistant-model: Claude Opus 5.5
Assistant-workflow: inline
Assistant-verification: bun test passed: 1749 tests, 2 PostgreSQL skips, 0 fail
Assistant-verification: bun run types passed: all workspaces and E2E
Assistant-verification: bun run ci passed: dprint, oxlint, tokens, type scale, Impeccable baseline
Assistant-verification: source check passed: @bastani/atomic 0.9.25-alpha.2 dist/builtin lists intercom, mcp, subagents, web-access, workflows
Co-authored-by: Alex Lavaee <lavaman131@github.com>