One shortcoming of SkylineCmd.exe which is often a nice way to run an instance of Skyline for which you know the location of the EXE (unlike the web installs that put the EXE in a hard-to-find location) is that using the instance to save a settings change: e.g. adding an external tool or using --save-settings, does not store the settings to the right user.config file, i.e. the one for the Skyline[-daily].exe in the same folder as the SkylineCmd.exe.

Agilent is currently solving this issue in their installer by simply running Skyline.exe directly and living without any output or exit code. This is clearly less than ideal.

We should add a command arg to SkylineRunner.exe to specify a path of the Skyline[-daily].exe to run. The way SkylineRunner runs Skyline.exe and uses a named pipe to pipe its output to standard out already works correctly for saving settings changes.

SkylineCmd.exe is still a great shortcut for all other command-line uses that do not require storing changes to user.config.

Skyline issues have moved to GitHub Issues at https://github.com/ProteoWizard/pwiz/issues
Issues will be ported as necessary for active work.