Bugfix/fix geometry warnings various bugs

• Ensure i1 is initialised and abort if a suitable value has not been found

• Expose write_gs2d routine

• Remove unused module level variables in ceq

• Remove commented out code

• Remove unused variable in deq.f90

• Remove commented out code, add a little documentation

• Remove commented out code

• Remove commented out code

• Remove unused variables in peq.fpp

• Remove commented out code in peq.fpp

First commit is the only place a potential bug was found, the other commits fix warnings, add documentation and try to make the code clearer by deleting comment out lines.