Especially for the Windows version, it would be great to be able to compile from the IDE. It should be simple to associate "C" files to whatever command line the user chooses (e.g. c:\dmars\scc.exe), and "PAS" files to another command line (e.g. c:\pascal\fpc.exe) and so on. But I haven't found such option.
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This is already supported. You can specify compiler and run commands for every supported filetype. Please read the manual (http://geany.uvena.de/manual/ch03s07.html). Unfortunately, the build system doesn't work at the moment under Windows. Only running commands is supported. Perhaps this will be better in the future.
I'll close this because under Unix systems it already works and for Windows it is on the TODO list.