[Vladimir Morozov (vmoroz)]

Description

Lets fork-sync roll a large, submodule-based upstream such as Chromium on a regular
cadence. Before this change, rolling a vendored Chromium subset from one release tag to the
next failed in several places: release tags are on separate branches and are not ancestors of
each other, new tags never reached the cached clone, tree:0 history fetches took close to an
hour and then failed, content from git submodules was invisible, and every sync re-added files
the fork had deliberately removed. AI merge had also gone stale: the configured Claude setup no
longer worked, and a retired model ID made every hunk fail.

Snapshot sync (fetchMode: "snapshot") — fetches only the base and target commits
(--depth=1) and merges two synthetic commits that contain just the synced scope, the target
parented on the base. The merge base is exactly the last synced commit, so release-tag rolls
work across branches (e.g. 149.0.7827.149 → 156.0.8078.48) without keeping an upstream
history cache. Tags resolve with ls-remote, and PR notes link the upstream range instead of
listing every commit.

Git submodules (submodules) — listed submodules are synced at the SHAs the upstream
commit pins, at both base and target. Their files are grafted into the synced tree, so 3-way
merge, conflicts, .syncignore, and deletions work on them unchanged, and pins can never drift
from upstream's. Optional fallbackUrls cover mirrors that dropped an old commit. URLs from
.gitmodules may not use the local file transport. PR notes list pin moves, URL changes, and
gitlinks that appeared, disappeared, or are not followed.

Pruned forks (keepLocalDeletions) — files the fork removed stay removed, new upstream
files are added, and only files that upstream deleted are deleted locally, so local-only files
are never touched. A newly configured submodule or sparse path is imported in full. fork-sync
also warns about vendored files hidden by .syncignore that would silently stop updating.

AI merge — the GitHub Copilot CLI is now the default provider, and its default model is
auto, so Copilot routes each request and no model ID goes stale. aiMerge.model accepts an
ordered list, and a model the CLI reports as unavailable falls back to the next entry with a
warning. A new reasoningEffort setting (default low, skipped for models that reject it)
keeps the two calls per hunk cheap. Also fixes hunks being rejected as context mismatches when
the conflict is followed by blank lines, e.g. near the end of a file.

Smaller fixes —

• sparsePaths entries may be files (e.g. LICENSE).
• History mode fetches a --tag or --commit that git fetch did not bring in, and caps the
  PR-notes commit table at 200 rows.
• Fetches skip submodule scanning, auto-gc, and commit-graph writing.
• --continue is safer: it refuses changed options, and the checkpoint is kept until the
  changes are applied.
• Output decoding no longer corrupts multi-byte paths split across pipe chunks.
• Paths are canonicalized, so syncs work when the repo is reached through an 8.3 short name,
  a junction or symlink, or a subst drive. Previously every listing failed with "is
  outside repository".
• Merge branch names stay unique when two syncs run within the same second.
• The package CLAUDE.md now points to a new AGENTS.md, as at the repo root.

History mode with none of the new options set behaves as before, apart from the fixes above.

Test plan

• New end-to-end tests run the CLI against local upstream fixtures. They cover the scenarios
  above: release branches, a whole-directory submodule served only by a fallback URL, unfollowed
  and newly appearing gitlinks, prunes, subDir, conflicts with --continue and --abort,
  switching modes, and config validation. Unit tests cover the new git plumbing, PR-notes
  formatting, and model fallback. yarn test passes, and the Copilot integration tests pass
  with RUN_INTEGRATION=1.
• Tried on a real Chromium subset with 9 followed submodules. Re-syncing the pinned tag is now a
  true no-op; before, it re-added about 3,000 removed files. A roll from 149.0.7827.149 to
  156.0.8078.48 completed the merge with 6 expected conflicts, all in files the fork modifies.
• To try snapshot mode, set "fetchMode": "snapshot" in a dependency's sync-config.json and
  run fork-sync --dep <name> --tag <tag>. See the README sections "Snapshot mode", "Git
  submodules", "Pruned forks", and "Choosing AI models".