You can use separate configuration directories for different projects and use the -c option to select which one you want. Then if you open files from the command line `geany -c config_with_project_1 file1` and `geany -c config_with_project_2 file2` will send the files to the specified instance. And when you close the instances they won't fight over which project and open files gets stored in the config file since each has its own :)
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