Set Thor min version to 1.0

[timothysmith0609]

What are you trying to accomplish with this PR?
Component of #658
I originally attempted to add the repeatable option to --filenames in this PR, but unfortunately there appears to be a bug (I suspect in Thor itself) that precludes that. I'm going to take a look at that after this PR merges.

Sets the lower bound of the Thor version we use to 1.0. This version includes parsing support for - as flag arguments (required to get rid of --stdin flag in favour of --filenames -).

How is this accomplished?

• Bump the lower bound for Thor in the gemspec
• Remove references in README for stdin, edit references to --filenames to indicate how to read from STDIN
• Update tests
• Fix code references

What could go wrong?
Small change across a module of the system (the CLI layer), so this should be a fairly safe and testable change. More difficult might be ensuring we clean up all references to the now-obsolete flags.

[dturn]

This isn't a Deprecations its a removal. Which I wasn't expecting, I though we'd just stop documenting it.

If we're going to remove it without a major version bump I think we need to have at least one minor version that supports both.

[timothysmith0609]

I though we'd just stop documenting it.

You're right, I was overzealous, here. I've added back the stdin flag to deploy, global-deploy, and render. The documentation still has all references to --stdin removed, so it's undocumented now. I've also made sure the tests exercise cases were we use either --filenames, --stdin, and their combination

I've also added a deprecation warning to the logs if we end up parsing the stdin option.