chore(tools): Fix hunk +Y offset when staging a subset of hunks

[JeanMertz]

When git diff-files --unified=0 emits hunks for a file, each hunk's +Y value reflects the cumulative line shift of every preceding unstaged hunk in that file. Staging only a subset of those hunks with git apply --cached --unidiff-zero uses +Y to position each change, so carrying over the full-diff offset causes the patch to land at the wrong line whenever unselected hunks contributed to the shift.

Two fixes are applied:

For git_stage_patch, a rewrite_hunk_y helper is introduced in hunk.rs that recomputes each selected hunk's +Y from the net line change of the preceding selected hunks only. A cumulative_offset accumulates (additions - removals) as hunks are assembled, and each header is rewritten before the patch is handed to git apply.

For git_stage_patch_lines, the HunkHeader struct previously preserved new_start from the original full-diff header and then applied it as an offset to the sub-hunk. That offset was wrong for the same reason. The field is removed and build_sub_hunk now derives new_start directly from the sub-hunk's own content: for replacements and pure removals it equals old_start; for pure insertions it equals old_start + 1.

Regression tests are added for both tools covering the scenario where an addition hunk is staged while an unrelated removal hunk higher in the file remains unstaged.