Add OS X proxy icon to title bar

Fixes #1891.

Test Plan:

  * Opened Atom window in directory, verified directory icon shows up
  * Opened a file and verified icon changed
  * Right clicked icon, verified menu appears
  * Drag file to terminal and it pastes the file path (yay)
  * Opened a new Atom window and opened some files in that to make sure that
    it didn't change the original window

I didn't add any specs for this - advice welcome here. I also haven't tested
on Windows or Linux but it looks like `setRepresentedFilename` is a noop on
those platforms.
path -> proxyIconPath

Test plan:
Crossed fingers
Implement setDocumentEdited too

As requested by @philipgiuliani

Test Plan:
Opened an existing file and made a modification. The icon fades at the same
time the tab close button changes to a circle. Undo makes the icon opaque
again.
Don't use project path as fallback icon for item with no path

Stops the project folder icon appearing in places that don't make sense
like settings and new files.

Test Plan:

  * Opened settings and didn't see the project folder icon
  * Closed all tabs and saw the project folder icon
Load the default themes in safe mode
Upgrade to atom-shell@0.15.4
Make menu bar auto-hide.
Upgrade to markdown-preview@0.97.0
Upgrade to language-yaml@0.15
Upgrade to language-sql@0.10
Fix indentation
Upgrade to markdown-preview@0.99
Move coffeelint settings to external file

The motivation is for this is to allow `coffeelint` config to be shared by
`script/grunt coffeelint`, global `coffeelint` and inline linting via
`AtomLinter`.

Test Plan:

Made some deliberate lint errors then ran `script/grunt coffeelint` and
verified the output looked the same with and without this change.
Update linux.md

Clarify the build steps. The most important is that initialy "Create ..." and "Install ..." could be interpreted as "(User should) create/install ..." while it should mean "(To) create/install ... (do)".
Revert "Make menu bar auto-hide."

This reverts commit 64731bff468fbefa01583cece573ddd1f00656c0.
Upgrade to atom-shell@0.15.5
Merge pull request #3196 from atom/atom-shell-v0.15.4

Upgrade to atom-shell@0.15.4
Upgrade to base16-tomorrow-dark-theme
Merge pull request #3219 from wernight/patch-1

Update linux.md
Upgrade to bracket-matcher@0.52