The problem was that some time ago when I couldnt find libsdl related packages, or didnt knew there names, I compiled them from source, this messed up my configuration and it created an alternate include directory in "/usr/local/include/SDL" which was being used rather than the default "/usr/include/SDL" and the SDL library which was in local/include folder had some files missing.
Aard on #tmw-dev pointed it out that "/usr/local/include/SDL" is being searched for SDL and it made things clear, so I removed SDL, reinstalled SDL reconfigured but still I had issues. Then I
altogether and reinstalled all libsdl related packages and then it worked.
I again thanks every one who has helped me, I learnt alot and if there's any one new to compiling tmw on linux please let me know I can help him for sure.