Oh and if those plugins are missing then it's the fault of your build system fork `geany-plugins`.
The build system doesn't enable any plugin if they have a missing dependency, but some plugins don't have any extra deps. It rather sounds like you didn't properly build GP against the Geany you just built, and it tried to install plugin files into the system's Geany's libdir (as it has to put them there for Geany to find them, even if it's outside PREFIX). best suggestion is to override `PKG_CONFIG_PATH` to point to the custom built Geany's *lib/pkgconfig*. Alternatively, use `--with-geany-libdir=PATH` configure option.