Separate config dependency bootstrap from install-time reconciliation. Only
reconciliation removes undeclared roots; diagnostic commands must retain them
so they can inspect the existing lockfile.
Share state loading, declared-root retention, and env graph pruning between
config dependency preparation and exclusion pruning. Load state before opening
the store and pass it into resolution. The Rust repeat-install fast path checks
this state so removing the last declaration cannot bypass cleanup.
Reuse existing verification, writing, and materialization for removals. Frozen
installs reject stale roots before mutation. Preserve package-manager roots,
including distinct versions of a package shared with config dependencies.
Keep Rust graph operations in the lockfile crate to avoid a dependency cycle.
Follow-up to pnpm/pnpm#17144.
Zoltan Kochan
d11a2a6a5a