Fix instability in dx-toolkit file/deepdirs test

Summary:
Adding a wait-for-close flag, when uploading a file. This is part of the dx-upload-all-outputs
script.

Test Plan: Existing tests, especially file/deepdirs.

Reviewers: klai

Reviewed By: klai

Subscribers: bagee

Differential Revision: https://phabricator.dnanexus.com/D160
Mock API debug tools
Java bindings: various environment-handling fixes

* DXHTTPRequest: better error message when no security context set
* DXJob.describe() now makes API call with custom environment if set
* New factory method DXProject.newProjectWithEnvironment to support
  setting custom environment
PTFM-12951 Move EE dependency installation code into dxpy
Java: compound ($and/$or) type queries when finding data objs

Summary:
* Introduce method FindDataObjectsRequestBuilder.withTypes
* Extract function serializeCompoundQuery

Test Plan: Unit tests. All existing and new tests passed.

Reviewers: pnguyen

Reviewed By: pnguyen

Differential Revision: https://phabricator.dnanexus.com/D158
[PTFM-13637] Don't append -lgcc_eh when CC=clang

Summary: * When building jq with clang, omit the -lgcc_eh flag to avoid an error from the compiler.

Test Plan: Performed test builds on an OS X 10.7 builder with gcc and clang, and on Ubuntu 14.04 with gcc.

Reviewers: psung

Reviewed By: psung

Subscribers: akislyuk

Differential Revision: https://phabricator.dnanexus.com/D164
Prevent weird output when code is wrapped in multiple "err_exit"s

Basically, the first err_exit will raise a SystemExit. The second and
subsequent ones should just pass that through unmolested.
Improve keyboard interrupt handling

Summary: Print "^C\n" instead of KeyboardInterrupt

Test Plan: existing tests

Reviewers: psung

Reviewed By: psung

Differential Revision: https://phabricator.dnanexus.com/D168
Preserve original stacktrace; obviates need for print-and-rethrow
PTFM-13536: confusing error by 'dx cp'

Summary: Refactoring of the 'dx cp' command, adding another test case to the test suite.

Test Plan: Additional test case added to the TestDXCp test suite.

Reviewers: klai

Reviewed By: klai

Differential Revision: https://phabricator.dnanexus.com/D169
PTFM-13829 dxpy.utils.normalize_timedelta: Interpret bare ints as seconds
Cosmetic formatting fixes
Fix typo in 30994a9
PTFM-13267: Exit gracefully by wrapping all dx methods in err_exit

Test Plan: existing tests and manual testing

Reviewers: psung, akislyuk

Reviewed By: psung, akislyuk

Differential Revision: https://phabricator.dnanexus.com/D170
PTFM-13864 Reconnect job log websocket client on 503
Remove extraneous log message

In a reconnect, this line will be reached synchronously later (just
before disconnecting), so the log message would be misleading.
Changed dx-verify-file -h exit code to 0
Changelog and version updates for v0.126.0
Cease building R packages for Debian

(cherry picked from commit ae41b29f54b44f6fb6fc8e3663cfe1e45364f961)
Changelog and version updates for v0.126.1