fix(server): generate PR diffs from the merge base

[sak0a]

When the PR base advances independently, a two-dot tree diff includes reversed base-only changes in the context sent to generatePrContent. A stale or missing local base can also inflate the context or fail despite an available tracking branch.

Generate stat and patch from a single explicitly resolved common ancestor, while retaining two-dot commit-log semantics. Reject histories with no common ancestor or multiple merge bases with actionable recovery guidance instead of generating misleading content. Invalid refs and other Git failures remain GitCommandErrors; existing truncation limits and markers are preserved.

For unqualified base branches, prefer an existing tracking ref from the intended repository (the head remote for same-repository PRs, origin for the existing fork workflow). Keep the PR target branch name unchanged and preserve explicit refs and local-only/custom base branches. This follows the merged upstream correction at pingdotgg/t3code#13170 and handles additional edge cases in Ryco.

Validation with pinned Bun 1.4.0 and bun install --frozen-lockfile:

• Original divergence reproduced before the fix: 3 files / 2 insertions / 2 deletions became only the feature file / 1 insertion.
• Real criss-cross history reproduced two common ancestors and an implicit Git diff that overstated the delta by one file; generation now rejects ambiguity. Unrelated histories now explain fetching/deepening history and choosing or transplanting onto the correct base.
• With tracking selection disabled, stale/custom/fork fixtures leaked a base commit and missing-local-base failed; local-only and explicit-local cases passed. All pass with the fix, including selection of the target repository instead of a fork's stale base.
• 46 focused tests passed (34.05s total), including existing PR workflows, ancestor/diverged/empty ranges, invalid refs and 59,000-byte patch truncation plus its marker.
• Server typecheck, format/check and lint for changed files, and git diff --check passed.

bun run --cwd apps/server test src/git/GitManager.test.ts src/vcs/GitVcsDriverCore.test.ts -t 'PR|readRangeContext'

Verification uses real Git in isolated temporary repositories; text generation and GitHub calls are faked. No dev server, browser session or live model-generated PR was exercised for this backend-only change, and full repository suites were not run. Tracking selection uses available conventional refs/remotes/<remote>/<base> refs; it does not force a new fetch or add custom fetch-refspec destination mapping.

The reported concurrent-destination worktree test flake was reproduced separately: both additions can fail with HEAD/index-lock errors. The same failure reproduced using only two concurrent git worktree add processes, without Ryco or PR range handling. This independent pre-existing issue remains; no worktree implementation or test semantics are changed here.

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