Undesired behavior when applying BPS patch to BIN/CUE ROMs

[dxman]

Paste the command

pnpm run igir move test clean report \
    --dat "${IGIR_LIBRARY_DIR}/dats/Redump/*.{dat,zip}" \
    --dat-name-regex-exclude "/Dreamcast/i" \
    --input "${IGIR_LIBRARY_DIR}/roms/Redump/" \
    "${INPUTS[@]}" \
    `# Let maxcso calculate CSO CRC32s, don't checksum compressed discs (we only care about the contents)` \
    --input-checksum-max CRC32 \
    --input-checksum-archives never \
    --patch "${IGIR_LIBRARY_DIR}/patches/ps/" \
    --output "${IGIR_LIBRARY_DIR}/roms/Redump/" \
    --clean-backup "${IGIR_LIBRARY_DIR}/clean/Redump/" \
    --temp-dir "/volume1/ramdisk/ramdisk/igir/temp/" \
    --dir-dat-name \
    --overwrite-invalid \
    --only-retail \
    --single \
    --prefer-language EN \
    --prefer-region USA,WORLD,EUR,JPN \
    --prefer-revision newer \
    --report-output "${IGIR_REPORTS_DIR}/Redump/igir_%YYYY-%MM-%DDT%HH:%mm:%ss.csv" \
    -vvv

Describe the bug

I have a library of PlayStation games that consist of ZIPed BIN and CUE files. Igir correctly identifies these files against Redump's DAT file and moves them into my library. However, when attempting to apply BPS patches to any of these games, I am running into a few undesired behaviors.

1. While the BIN/CUE files are in a ZIP, Igir does not recognize the matching CRC32 values to apply the patch. (See provided igir-1.log)
2. If I unzip the BIN/CUE files, Igir correctly matches the patch to the BIN file. However, it copies the original CUE file as-is, so it does not work with the newly-patched/renamed BIN file. (See provided igir-2.log)

Expected behavior

The behaviors below would be the "ideal", but if they are currently officially unsupported and/or qualify as feature requests, it probably wouldn't be a bad idea to document the current behavior to avoid confusion.

1. Igir matches the BIN file within the ZIP file to the BPS patch, using CRC32, and outputs a ZIP file containing the patched BIN/CUE.
2. When applying patches to BIN files, Igir correctly outputs a CUE file that is compatible with the patched BIN. This would involve doing a find/replace of the text within the CUE file, as well as renaming the CUE file to have the same base (minus extension) name.

Debug logs

igir-1.log
igir-2.log

DAT(s) used

Redump

igir version

3.0.1

Node.js version

22.9.0 (via PNPM 9.11.0)

Operating system

Linux (Synology NAS)

Additional context

No response