fix: retry repository ref updates after concurrent pushes

[lorenzozanee]

Summary

Retry repository file-operation ref updates after concurrent pushes by rebuilding the change from the latest branch tip.

Why

A concurrent writer can advance a branch between the initial read and the non-force ref update, causing the prepared commit to be rejected.
Fixes #2481

What changed

• Share tree, commit, and ref-update logic between push_files and delete_file.
• Retry fast-forward conflicts by reading the current branch tip and rebuilding the commit.
• Normalize file argument encodings accepted by MCP hosts.

MCP impact

• No tool or API changes
• Tool schema or behavior changed
• New tool added

Prompts tested (tool changes only)

Security / limits

• No security or limits impact
• Auth / permissions considered
• Data exposure, filtering, or token/size limits considered

Tool renaming

• I am renaming tools as part of this PR (e.g. a part of a consolidation effort)
  • I have added the new tool aliases in deprecated_tool_aliases.go
• I am not renaming tools as part of this PR

Note: if you're renaming tools, you must add the tool aliases. For more information on how to do so, please refer to the official docs.

Lint & tests

• Linted locally with ./script/lint
• Tested locally with ./script/test

Docs

• Not needed
• Updated (README / docs / examples)