Formatting and documentation cleanup; remove obsolete testProjectPermissions function (resolveProject was modified to only return projects with at least CONTRIBUTE access).
Fix improper cast (resulted in warning about signed vs. unsigned integer comparison).
Use C-style comments in C files to get rid of warnings.
Formatting and log cleanup.
Change minimum permission level from CONTRIBUTE to UPLOAD.
More formatting cleanup.
Formatting/cleanup; remove some unnecessary includes from header file.
Move include guards into header file where they belong.
Formatting; remove a function from the header file that didn't need to be exposed there.
Formatting.
Formatting; remove an unnecessary reference to the options object.
Formatting.
Rearrange some code; pass the options object to some methods that need it, instead of making it global across modules.
[PTFM-9696] Print a useful error message when an input is not a regular file.
Formatting.
Remove lots of relatively useless log messages to make verbose output less verbose.
Merge branch 'jdale-ua-cleanup' of github.com:dnanexus/dx-toolkit into jdale-ua-cleanup