Avoid corruption of binary files embedded in gzip, bz2 and zip archives in the upload tool.

Add an option in the upload tool to disable the conversion of universal
line endings to Posix line endings.
This is useful for avoiding corruption of uploaded files when a binary
file is contained inside a gzip, bz2 and zip archive.

This fixes bug report: https://trello.com/card/issue-with-uploaded-2bit-gz-files/506338ce32ae458f6d15e4b3/702
When setting external metadata using _handle_metadata_externally (e.g. local and lwr runners) use the requirments of the set metadata tool to determine dependencies. Resolves issue seen with missing samtools command when samtools is not in the path, but has been installed with the dependency system.
Use null object pattern to simplify logic related to no dependency manager being set.
Fixes bug introduced in 4241eff related to dependency_manager being None if tool_dependency_dir is not set.
Close search branch.
Default merge
Adding update_time to ldda to_dict
Adding update_time to hda to_dict
javascript library and modal refactoring, automatic even binding if flag provided
Merged in kellrott/galaxy-central/search (pull request #296)

Adding update_time to dataset to_dict methods
Charts: Show chart creation form on startup, add pie chart
Merge
Charts: Improve button selection
PEP-8 and unused variables fixes.
Let /api/workflows show() method display also importable workflows.
Add show_published param to /api/workflows index() method to display also published workflows.
Move core code for importing a shared workflow to UsesStoredWorkflowMixin.
Add /api/workflows/import method to import a workflow shared by other users.
Explicitly require UsesAnnotations mixin for the annotations api controller *after* UsesStoredWorkflowMixin.
Add tool execution tests for various exceptional conditions.
Tool action raising exception, redirecting, and returning an error message.
Rearrange __handle_execute and handle_input in Tool...
Slightly cleaner this way (fewer exit points) and will enable extensions I am making downstream.