Fixing --debug deleting temporary files.
fixed ConfigurationSubstitutionVisitor
Merge pull request #1107 from kframework/keepTempFiles

Fixing --debug deleting temporary files.
Merge pull request #1108 from yilongli/fix-cfgsubstvisitor

fixed ConfigurationSubstitutionVisitor
Merge branch 'master' into sdfCrashMessage
Using RuntimeException instead of just Exception.