Two DATA-LOSS bugs in ShellFileOperations found in a core-tools audit,
each reproduced live against current main:
1. Non-UTF-8 file content silently corrupted on read->write. The terminal
env decodes stdout with errors='replace', so a latin-1/8859 file's bytes
arrive as U+FFFD before _is_likely_binary inspects them. U+FFFD is
'printable', so the >30%-non-printable check never flagged it, and the
agent would read the mojibake and write it back, permanently replacing the
original bytes. Fix: treat a sample containing U+FFFD as binary (read-only).
2. Writing through a symlink destroyed the link and orphaned the target. The
atomic temp-file + 'mv -f' swap replaced the symlink itself with a plain
file; the real target was never updated. Fix: resolve the link with
readlink -f/realpath first and recompute the temp dir from the resolved
target so the mv stays same-filesystem atomic. Broken links fall back to
the original path (no regression).
Both verified with sabotage-checked regression tests (fail without the fix).
Proper UTF-8 text (incl. non-ASCII) and plain-file writes are unaffected.
