Fix error handling for setting executable in dx add/update stage
Improve dx describe workflow and better error handling

- IO specs displayed when describing by name
- Inaccessible stages rendered as such in describe, list stages
- dx run refuses to run a workflow with inaccessible stages
Remove extraneous TODO comment
Re-enable tests that depend on now-released features
Temporarily skip tests that require unreleased features
Fix DXDataObject.closeAndWait
Allow supplying terminateJobs to DXProject.terminate
Remaining data object classes: DXFile, DXGTable, DXApplet, DXWorkflow

* DXGTable, DXFile, DXApplet, and DXWorkflow are mostly intended for
  obtaining handles to existing data objects. For example, no high-level
  bindings are provided for uploading or downloading file data, or
  adding or getting GTable rows.
* Add JSON (de)serializers for data object classes.
* Support for test configuration variables.
Add more test configuration flags. Minor Javadoc fixups.
Java low-level bindings with automatic (de)serialization.
Java high-level bindings use newly provided low-level bindings.
[PTFM-10293] Fix dx find executions -n > 999
Add test for previous commit
Changelog and version updates for v0.79.0
R build fix: install roxygen2 from archive.

* Update outdated R documentation pages.
Changelog and version updates for v0.79.1
Fill in Java changelog belatedly.
"dx get applet-xxxx" reconstructs the app source directory

* Thanks to George for the initial code
* Fix exit codes for some other invocations of "dx get"
* Add tests
[PTFM-10388] Fix and test for dx get record --no-ext
PTFM-10340: dx-app-wizard now creates empty authorizedUsers entry