Remove trailing whitespace.
Move Java build docs to src/java/Readme.md and add test instructions.
Some more tab completion fixups

Also, add the DXTEST_ENV variable for running Python tests which will
clobber your local environment (.dnanexus_config files, etc.)
Fix duplicated line.
Linkify some Python cross-references.
Mention the "UPLOAD" permission level in discussions of permissions.
Ensure details is a hash before doing a key lookup.
Replace C++-style comments with C-style comments to eliminate warnings.
Fix compiler warning (bad cast leading to signed vs. unsigned comparison).
Remove unused code.
Change minimum required permission level from CONTRIBUTE to UPLOAD.
Remove some unnecessary includes.
Hide a function that doesn't need to be exposed in the Chunk interface; remove some unnecessary includes.
Ensure that all header files have include guards; remove more unnecessary includes.
Options object should not be a global variable; pass it to a couple of functions that need it.
[PTFM-9696] (Again.) Print a useful message when a file argument is a directory, or is not a regular file.
Clarify explicit_perms and public flags for find_projects.
Document dynamically filled attributes of DXGTable, DXApplet objects.
Fix broken DXApp:addTags,removeTags methods.
Rename DXApp.{add,remove}Tags to follow naming conventions.

Leave behind transitional methods.