LGTM: Fixing the vast majority of open issues

[Windchild292]

This fixes all but four of the current LGTM issues for MML, including multiple resource leaks.

Once this is merged I'll fix the final four issues.

To Review:
Whitespace differences off, as I also fixed some whitespace problems.

[lgtm-com]

This pull request fixes 12 alerts when merging 9b8f76c into 4849775 - view on LGTM.com

fixed alerts:

• 7 for Dereferenced variable may be null
• 3 for Potential input resource leak
• 2 for Boxed variable is never null

[lgtm-com]

This pull request fixes 26 alerts when merging f3f7c02 into 4849775 - view on LGTM.com

fixed alerts:

• 10 for Implicit narrowing conversion in compound assignment
• 8 for Dereferenced variable may be null
• 3 for Potential input resource leak
• 2 for Useless comparison test
• 2 for Boxed variable is never null
• 1 for Contradictory type checks

[Windchild292]

I'm considering this no longer a draft given it fixes 26 of the 30 issues, and will open a PR shortly after this is merged to handle the final four issues.

[SJuliez]

All good.