Fix most of the issues and test cases (see description)

[LemonBreezes]

This PR fixes #43, #41, #39, and partially addresses #40 by fixing most of the test cases. Now only 7/1093 of the test cases fail. I also made a few fixes that have not been reported as issues yet.

I believe that the remaining test cases need to be reviewed because some of them (I believe) are being executed correctly but the expected result is incorrect.