fix(core): honor End of File hunks when the file ends in a newline - #4661

Summary

apply_diff is how sandbox agents edit files. *** End of File hunks were silently wrong on almost every real source file because those files end in a newline.

str.split("\n") keeps a trailing empty element for newline-terminated text. EOF matching treated that phantom as a real line, so:

1. An append at EOF inserted a blank line and dropped the trailing newline ("a\nb\n" + +c became "a\nb\n\nc" instead of "a\nb\nc\n").
2. Repeated context with an EOF marker matched the first occurrence, not the last.

The same locator is used by sandbox apply_patch, so this is not a helper-only issue. Agents could apply a plausible patch and leave the wrong code in the workspace with no error.

The locator now ignores that terminator when eof=True. Existing non-EOF and CRLF behavior is unchanged.

Fixes #4660

Test plan

• python -m pytest tests/test_apply_diff.py tests/test_apply_diff_helpers.py
  • 31 passed, including EOF append, last-occurrence context, CRLF, and helper coverage for the phantom split element