feat(cli): add vfs seed for portable dirty-base capture

[factory-ain3sh]

Description

What

Adds vfs seed <session-id> --pin <commit>: captures a run session's live git state (dirty and untracked files, deletions, local commits, index) into its portable delta without mounting. vfs run --session <id> --seed-pin <commit> is the atomic startup form.

Why

A session created on a dirty checkout only sees that dirty state through overlay base read-through, which does not travel. Without seed, a receiver materializing the packed delta over a pristine checkout at the pin would silently lose the sender's uncommitted work. Capture-by-construction from birth is the design; seed extends it to bases that were already dirty at session start.

How

Seed diffs the base checkout against --pin and imports through the core bulk-import API (no FUSE/NFS mount):

• Dirty and untracked files import as delta content; paths deleted since the pin become whiteouts. Ignored files stay base-local (git status --untracked-files=all).
• Local-only commits ship as a compact git pack plus HEAD and the current branch ref under delta .git/ paths; the sender's index bytes come along, preserving staged-vs-unstaged state.
• Writes go to a private staging database, published only after import, whiteouts, metadata, and finalization all succeed; a failed seed leaves the live delta retryable.
• Birth-time only: a second seed fails with session already seeded; a live session fails with the same exit-3 gate as pack.

Stack (merged bottom-up 2026-07-28, vfs main @ 3b2af42):

1. refactor: rename agentfs to vfs across runtime, tooling, and docs #4 rename agentfs to vfs
2. feat(cli): add vfs pack for atomic session transfer artifacts #5 vfs pack
3. feat(cli): add vfs seed for portable dirty-base capture #6 vfs seed <- this PR
4. feat(cli): harden resumable run sessions and add status preflight #7 run hardening + status

Related Issue

Part of AC-768

Reviewer Guide

Diff shape: ~80% cmd/seed.rs, ~10% run/ integration (--seed-pin lock choreography), ~10% core overlay/session support.
Review depth: Deep on the git-state capture matrix; the correctness question is "which sender states round-trip".
Read order:

1. crates/vfs-cli/src/cmd/seed.rs — status enumeration, bulk import, whiteout recording, git pack + index capture, staging publish
2. crates/vfs-cli/src/cmd/run/linux.rs + darwin.rs — exclusive-create-then-downgrade-to-shared lock ordering for --seed-pin
3. crates/vfs-core/src/fs/overlay/mod.rs — whiteout API surface seed relies on
4. docs/MANUAL.md — the portable-state contract (ignored files excluded, index revalidation semantics)

Open for pushback: copying raw index bytes rather than regenerating the index on the receiver. Git revalidates cached stat fields against the pristine checkout at the pin, so stale stats self-heal, but it is the least obvious part of the contract.

Risk & Impact

Seed writes into the session delta, so a capture bug corrupts portable state at birth; the staging-then-publish structure bounds that to "seed failed, retry" rather than a half-seeded live delta. The exclusion of ignored files is deliberate scope (build outputs and caches stay base-local) and is documented as the portable-state boundary.

Verification

Behavior verified. Dirty file, untracked file, deleted-since-pin, staged-vs-unstaged, and local-commit states round-trip to a receiver materialization over a pristine pin checkout; second seed and live-session seed fail with the documented errors (verified @ 10507f1).
Regression coverage. CLI suite exercises the seed state matrix and the exit-code gates; core tests pin whiteout semantics.
Not tested. Submodule-containing worktrees; out of scope for the MVP contract and rejected by the state enumeration rather than mishandled.
Standard validators. cargo build/test and CLI shell suites clean.