do not overwrite proof-shell-quit-timeout by default (final PG 4.1 supposedly gets it right);
#main object logics
src/Pure
src/FOL
src/HOL
src/ZF
src/CCL
src/CTT
src/Cube
src/FOLP
src/LCF
src/Sequents
#misc components
src/Tools/Code
src/Tools/WWW_Find
src/HOL/Tools/ATP
src/HOL/Mirabelle
src/HOL/Library/Sum_of_Squares
src/HOL/Tools/SMT
src/HOL/Tools/Predicate_Compile
src/HOL/Mutabelle