The information in the howto on https://wiki.geany.org/howtos/win32/msys2 were pretty old and also partly outdated. Some months ago, I started to rewrite the howto to be more accurate and recent. It took some time but I could finally finish it (except the release.py scripts, I forgot to copy them from my Windows machine, will do in a few days).

The updated howto now also uses osslsigncode for code signing which is easier to install and use than the Microsoft SignCode tool.

Some remarks regarding your mentioned problems above:

it's way easier to do anything regarding compilation and installation from within a MSYS2 shell - using the native Windows command prompt is not been tested and supported and probably makes things just more complicated
the release scripts and especially the code signing is not important for you, these steps are only necessary if you would build a full binary release for distribution but for local development I recommend to skip these steps

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