Resolve remaining unit test failures.

Update the remaining unit tests following the many design changes.  The unit tests should next be factored to use repository_tool.py, avoid pseudo repositories and repository objects, monkey patching, etc.
Update METADATA.md.

Re-word sentence and update outdated rolenames.  Add note about out-of-date metadata content and names in the listed examples.
Update test_extraneous_dependencies_attack.py.

Remove text inserted and improperly removed from a previous merge conflict.
Update README.md.

Update the expected use of the repository_tool.py module and list the modules that may be used in TUF integrations, which the repository tool does not handle.Rewrite the sentence that mentions the integration tools so that it does not appear to be out of context.
Add disclaimer for deprecated latex documents.
Fix updater.py typo.
Update tuf-spec.txt.

Incorporate recent design changes, such as a role name change, supported signature schemes, and expected metadata extension.
Fix for issue #171.
Update repository_tool.py.

Add missing comments for three of the arguments in generate_snapshot_metadata()'s docstring.
Expand docstring comment in non-public function and mention that temporary metadata is generated to a temporary location.
Minor cosmetic changes.
Update repository_tool.py.

Raise exception if signature not found in remove_signature().
Minor edits to comments and whitespace.
Update tuf-spec.txt
Implement key format requested in issue #171.

Exclude the 'private' attribute from metadata key objects, and when calculating keyids.
Merge branch 'repository-tools' of https://github.com/theupdateframework/tuf into repository-tools
Update repository_tool.py.

Exclude the invalid metadata object included when a repository.write() exception is raised.
Update README.md

Modify the exception raised by repository.write() in the `Create Root` section.
Merge branch 'repository-tools' of github.com:theupdateframework/tuf into developer-tools
Added the layout_type variable, fixed some stability issues
The layout_type flag is used to decide whether a regular directory
structure is going to be used. This means, that if the targets folder is
under the metadata_directory tree or not. This flag lets the project
module decide in which places to locate metadata (i.e. if it needs a
metadata subdirectory or not).

Also fixed stability issues, in which the delegated target files didn't
lose their prefix.
Clean up of some commented lines