refactor: apply retry at individual API call sites inside createTree

[c-vigo]

Context

Follow-up from PR #23 review: commitViaAPI wraps the entire createTree(...) call in withRetry. createTree can perform many REST calls (createBlob, chained createTree). A retry after a mid-way transient failure re-runs the whole operation and can re-upload blobs/trees, increasing API usage and rate-limit pressure.

Proposal

Apply withRetry at individual Octokit REST call sites inside createTree and createTreeChained (or thread RetryConfig into helpers) instead of retrying the whole multi-call operation.

Tradeoffs

• Pro: Finer-grained retries avoid redoing successful work after a failure late in the batch.
• Con: Requires threading retry config through internal helpers and more surface area for tests.

Related

• Copilot review comment on src/commit.ts (coarse createTree wrap)