[PTFM-4820] Various dxcpp changes (may break existing code):
  - All handler classes, and helper functions, etc are in namespace dx now
  - g_* are no longer global variables, but rather created on first use (present in dx::config)
  - Configurable user-agent string in dxcpp (by default dx-toolkit version is used)
  - UA & dx-verify-file have been fixed to use params in dx::config, instead of g_*
  - Various other small fixes
Merge pull request #13 from dnanexus/PTFM-4820-dxcpp-refactoring

[PTFM-4820] dxcpp refactoring
PTFM-4952 Retry logic in Java bindings.
PTFM-4952 Load DNAnexus environment from JSON config.

Refactor the loading and storage of the environment variables into a new
class DXEnvironment.
Merge pull request #14 from dnanexus/PTFM-4952-java-bindings

Improvements to Java bindings
Presumably more efficient way of obtaining the UTF8-encoded length.
Fixing some dxcpp warnings generated by clang
  - Note: dxcpp compiles fine using clang v3.2 for ubuntu
Adding handling of SV fields marked as other
Merge branch 'master' of https://github.com/dnanexus/dx-toolkit
Export ALT header field information
R: Removing version # from build process; modifying by hand now
R: fixing up doc_R target so that DESCRIPTION is in the html directory
R: adding a line to .gitignore
Changelog update for v0.38.0
Adding 'User-Agent' header to  dxpy requests
Add utils to support builder pattern for creating JSON objects.

This permits building JSON objects with a lot less casting (or temporary
variables).

Updated example Java apps to show how the builder can be used.
[PTFM-5674] Upload Agent now calls /system/greet to check for updates (and version bumped to v1.2.4). Other changes
  - Added /system/greet to api_wrappers
Remove stdout/stderr fields from dx job describe formatter
Fix wiki link.
[PTFM-5184] UA now uses "file" to determine mime type on POSIX systems
  - Various fall back mechanisms are also available
  - Code refactored