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CMD crashes with a NullReferenceException at both interactive prompts when stdin is not a console

Status: Open.

#2770 In smith-chem-wisc/MetaMorpheus;

· trishorts opened on Aug 28, 2026

Two more data files are missing from the MSI, and the installer-contents check only compares DLLs

Status: Open.

#2769 In smith-chem-wisc/MetaMorpheus;

· trishorts opened on Aug 28, 2026

XLSearchTask rebuilds each partition's peptide index N times in the second-round pairing loop

Status: Open.

#2768 In smith-chem-wisc/MetaMorpheus;

· trishorts opened on Aug 28, 2026

RNA XML loading passes the thread count as the heterozygous-variant limit

Status: Open.

#2762 In smith-chem-wisc/MetaMorpheus;

· acesnik opened on Aug 27, 2026

CMD: startup ErrorsReadingMods are silently dropped when no XML database is supplied

Status: Open.

#2757 In smith-chem-wisc/MetaMorpheus;

· trishorts opened on Aug 25, 2026

Custom monosaccharides are lost on install/upgrade: MonosaccharidesCustom.tsv is installer-managed under OVERWRITEAPPDATA

Status: Open.

#2752 In smith-chem-wisc/MetaMorpheus;

· trishorts opened on Aug 24, 2026

Migrate off retired protease names when mzLib #1186 lands (bare 'trypsin' changes meaning; GUI switch cases already dead)

Status: Open.

#2750 In smith-chem-wisc/MetaMorpheus;

· trishorts opened on Aug 20, 2026

MzIdentMLWriter over-allocates six child arrays and hardcodes a 500-item cap

Status: Open.

#2734 In smith-chem-wisc/MetaMorpheus;

· trishorts opened on Aug 17, 2026

SILAC post-quantification re-keys FlashLFQ peptides outside the quantification allow-list, leaving the results object unsafe to re-quantify

Status: Open.

#2719 In smith-chem-wisc/MetaMorpheus;

· trishorts opened on Aug 13, 2026

Custom crosslinkers silently lose EThcD when saved and reloaded

Status: Open.

#2716 In smith-chem-wisc/MetaMorpheus;

· acesnik opened on Aug 12, 2026

Installer neither installs nor checks for a .NET runtime

Status: Open.

#2714 In smith-chem-wisc/MetaMorpheus;

· acesnik opened on Aug 12, 2026

arm64: IsoDec and Bruker inputs fail without a diagnosable message

Status: Open.

#2702 In smith-chem-wisc/MetaMorpheus;

· acesnik opened on Aug 3, 2026