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.
Add retry heuristic for slow futures and enable it for file downloads
Quick Java fixups.

* Remove unused imports
* API methods are static methods of DXAPI
* Test classes declare package com.dnanexus
java wrappers: enable override of security context on a per-DXHTTPRequest basis