I'd vote rather for a more generic phrasing.
/usr/share should be right for most users as this is usually the path used by distro packages. /usr/local/share is the default if you compile from source yourself and do not specify an installation prefix, this is not the way most users do install Geany, I guess.
Those users who install Geany from source and use a custom prefix, probably know what they are doing and so also can mentally replace the provided default path in the documentation/README with that they used for ./configure.

In the documentation, we already have a few paragraphs about different config/resource file paths, see http://geany.org/manual/#configuration-file-paths. Maybe we could just refer to this part of the docs in the README?

Something like "$PREFIX" could rather increase confusion for users rather than solving it.

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