Hi Sadik,
Of course you may know all the above already. If so, you need to build your fork of CDT. The full solution would be to setup your own build environment and use maven - but that may seem overkill.
What does not work, AFAIK, is exporting just the plug-in[0]. You need to export a feature and include a P2 repo. You can use org.eclipse.cdt.platform-feature, that is the smallest feature that includes org.eclipse.cdt.core [1]. When you export the feature, include a P2 repo:
eclipse -application "org.eclipse.cdt.core.GeneratePDOM" -data workspace -noSplash -consoleLog [... options ...]
I hope that this was helpful and you will consider contributing back your improvements to GeneratePDOM.
Jonah
[0] In theory this should work adding the jar to the dropins directory. That seems hit and miss as reported by others on this mailing list.
[1] You can try to write your own feature by using org.eclipse.cdt.platform-feature as a starting point and including only the minimum necessary, probably org.eclipse.cdt.core as a plug-in and the org.eclipse.cdt.native feature.
[2] You may have trouble installing this into an Eclipse installation that already has CDT in it due to version issues.