Add file mode (executable bit) support to `push_files`

pkg/github/repositories.go の push_files ツールの定義と、Git Data API のツリーエントリを構築するループから始めます。files[] の入力スキーマと既存のデフォルト値を追跡し、受け付けられるモードとモードを省略した場合の動作が一貫して表現されていることを確認します。完了条件は、push_files が要求されたモードを保持でき、デフォルト値の互換性が維持され、create_or_update_file がスコープ外のままであることです。

Feature request: expose file mode (executable bit) on push_files

Use case

Agentic coding harnesses use this MCP server to publish files into a repo
on behalf of an LLM (issue execution, autonomous PR workflows, etc.).
When the work the agent is asked to produce is a shell script, build
helper, or other executable, the resulting file needs the executable
bit set (100755) — otherwise reviewers either have to chmod +x after
merge or merge a broken artifact.

Today there is no way for an MCP client to land an executable file
through this server. Both file-write tools use APIs that surface a fixed
mode:

• create_or_update_file → Contents API (PUT /repos/.../contents/{path}),
  which always writes mode 100644. This is a GitHub API limitation, not
  something this server can route around.
• push_files → Git Data API (CreateTree + CreateCommit +
  UpdateRef). The underlying API does support per-entry mode, but
  the tool's input schema doesn't expose it. Each entry is currently
  {content, path} only.

We've observed agents react to this in two unhelpful ways:

1. Quiet hallucination. The agent reports in the PR body that it
   pushed with mode 100755 when in fact the blob landed as 100644.
2. Workaround scope drift. The agent invents a second file (e.g.
   scripts/permissions.sh containing find scripts/ -exec chmod +x)
   that wasn't part of the task, hoping a CI step or human will run it.

A first-class mode parameter on push_files would close both failure
modes cleanly.

Proposed change

Extend the push_files.files[] input schema with an optional mode
field, validated against the set the Git Data API accepts:

Mode	Meaning
100644	regular file (default if omitted)
100755	executable file
120000	symlink
040000	subdirectory (subtree)
160000	submodule

For most agentic use cases only 100644 (default) and 100755 matter,
but echoing the full Git Data API set keeps parity with the underlying
endpoint.

Backwards compatible: existing callers that omit mode get 100644,
which is what they get today.

Implementation pointer

The relevant code is already calling Git.CreateTree with a
[]*github.TreeEntry (in pkg/github/repositories.go, around the
PushFiles tool definition). The go-github TreeEntry struct
already has a Mode *string field — it just isn't being set from the
tool input. Threading it through should be a small change:

// in the loop that builds entries:
mode := "100644"
if f.Mode != nil {
    mode = *f.Mode
}
entries = append(entries, &github.TreeEntry{
    Path: github.String(f.Path),
    Mode: github.String(mode),
    Type: github.String("blob"),
    Content: github.String(f.Content),
})

Plus input-schema additions for the optional field with the validated
set above.

Single-file case

create_or_update_file can't be fixed the same way because the Contents
API doesn't support mode at all — it's a GitHub API constraint, not a
server constraint. For the single-file executable case, callers can use
push_files with a one-entry files array. Worth noting that in the
tool's description so clients pick the right call.

Out of scope

• Changes to create_or_update_file (blocked by Contents API).
• Symlink/submodule write flows beyond just accepting their modes on the
  schema.
• Validating the executable-bit semantics on the receiving end.

Context

Filed against this server because we've been hitting the limitation
from a Claude-Code-plans / Goose-executes harness
(why-pengo/claude_and_goose),
where local-model executors are asked to ship small bash helpers as
part of issue-driven PRs. Happy to send a PR if the proposed shape
looks right.