Replace custom os/exec-based command execution with
github.com/sourcegraph/run. The new implementation delegates process
lifecycle management to the library while preserving the existing public
API and all behavioral contracts (timeout, cancellation, stderr
handling, debug logging).

Key changes in command.go:
- Replace exec.CommandContext with run.Cmd, using run.Arg to quote
  arguments for the shell-based parser
- Add newRunCmd helper to centralize run.Command construction
- Simplify RunInDirWithOptions by streaming stdout via Output.Stream
  and extracting stderr from the error
- Optimize RunInDir to stream directly to a bytes.Buffer, preserving
  raw bytes (important for binary-ish output like ls-tree -z)

Convert repo_tree.go LsTree to use gitRun with local args, removing
the last NewCommand call site. Rewrite command_test.go to test the
new gitRun/gitPipeline helpers directly, removing tests for the
deleted Command struct.

Fix timeout context cancel leakage, tighten exit-status matching, remove fragile
stderr re-concatenation paths, and harden author/diff argument handling.

- Fix exit status matching: replace loose HasPrefix with isExitStatus
  helper that won't match "exit status 1" against "exit status 128"
- Fix opt.Args ordering in ShowRefVerify and DeleteTag: move before
  --end-of-options so flag args work correctly
- Fix gitRun log capture: capture partial stdout on error instead of
  logging empty output for failed commands
- Quote args with special characters in log output for readability
- Fix repo_pull_test: "bad_revision" causes exit 128, not exit 1

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

- Remove nil check on ctx in gitCmd (callers always provide non-nil ctx)
- Remove stdin parameter from gitPipeline (no production caller uses it)
- Rewrite isExitStatus to use run.ExitCoder interface instead of string
  parsing, as suggested by reviewer
- Remove unused errors and os/exec imports
- Update tests to use gitCmd directly for stdin-based scenarios

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

- Rename helpers: gitCmd -> cmd, gitRun -> exec, gitPipeline -> pipe
- Remove stderr parameter from pipe (stderr is already in the error)
- Remove extractStderr (no longer used after stderr removal)
- Remove Blob.Pipeline stderr parameter and update all callers
- Rename CreateArchive -> Archive and add --end-of-options

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>