If you notice performance issues specifying lots of input files on the command line with Windows, i.e. a creep in memory use with corresponding CPU usage degredation, there's a way to avoid the problem. You can do this by creating a wrapper script batch program which is just a text file with a ".bat" file extension. Name it something like "runcomet.bat" with the contents as below and execute it instead of executing Comet directly i.e. "runcomet.bat *.mzXML". By running such a batch script, it will invoke individual, sequential instances of Comet to search all input files.

Contents of runcomet.bat (you can save-link to file):   for %%A in (%*) do ( comet.exe %%A )

Specify the full path to the comet.exe binary in the batch file if it does not reside in the same directory as the command is being executed.

For linux, try:   find . -name '*.mzXML' -print | xargs comet.
Or try this simple runcomet.sh bash script. Download it, make it executable with "chmod +x runcomet.sh" and place it somewhere in your PATH. Then run searches using "runcomet.sh *.mzXML". This script expects the binary named "comet" to also be in your path.