Now a parameter in AppSettings.config of web app and App.config in Inca called ServerCompanyHomeFolder can be specified. (example <add key="ServerCompanyHomeFolder" value="d:companyfolderInca"/>)

This parameter specifies local path where following folders are stored:

1. "libraries" folder – copy of "libraries" folder of datahome folder (all libraries are automatically synced on app start and before script compilation)
2. "AssemblyCache" folder – stores libraries for all compiled user defined scripts (library compiled for each script on first execution)
3. "TF-Compiler" folder – folder which stores temp files needed during script compilation (normally if app is not in script debug mode(parameter with id 392 ScriptDebugMode) should be empty)

If this parameter is not specified, all folders mentioned above are stored for web app directly in datahome folder. For Inca in "(datahomefolder)/Inca".

You should specify different folders for WebApp and Inca. However one folder can be subfolder for another, for example

App.config:
<add key="ServerCompanyHomeFolder" value="d:companyfolderInca"/>

AppSettings.config
<add key="ServerCompanyHomeFolder" value="d:companyfolder"/>