This is would be wrong. The version specifies the desktop-entry-spec form Freedesktop.org. There is no 0.10 version, there is however a Version 1.0. This version has nothing to do with the version of the application this starter starts.
Use a Theme with an application icon matching the name gephi or add this icon to your Theme.
There’s nothing wrong with the desktop file, just a couple harmless warnings:
❯ desktop-file-validate gephi.desktop
gephi.desktop: warning: value "Application" for key "Categories" in group "Desktop Entry" contains a deprecated value "Application"
gephi.desktop: hint: value "Application" for key "Categories" in group "Desktop Entry" does not contain a registered main category; application might only show up in a "catch-all" section of the application menu
Of course. gendesk is not required to use gephi . A normal user doesn’t need this package. Therefore it is not a dependency.
gendesk is only required if you want to use the PKGBUILD file to build your own package of gephi. If you use makepkg with this PKGBUILD for gephi, the make dependencies will be installed.
Had you reported what the issue actually was instead of your imagined solution, they would have looked into it. I’ve edited your topic title to be clear about what it is.