Issue 1:
I'm not sure what the best medium to have this discussion in, so let's just use an issue for now.

WorkspaceView

Add

WorkspaceView::eachPaneView # Rename of WorkspaceView::eachPane

WorkspaceView::getPaneViews # Rename of WorkspaceView::getPanes

Keep

WorkspaceView::appendToBottom

WorkspaceView::appendToLeft

WorkspaceView::appendToRight

WorkspaceView::appendToTop

WorkspaceView::prependToBottom

WorkspaceView::prependToLeft

WorkspaceView::prependToRight

WorkspaceView::prependToTop

WorkspaceView::eachEditorView

WorkspaceView::getActivePaneView

WorkspaceView::setTitle

WorkspaceView::updateTitle

Deprecate or Remove

WorkspaceView::getPanes # Renamed

WorkspaceView::eachPane # Renamed

WorkspaceView::confirmClose

WorkspaceView::focusNextPane

WorkspaceView::focusPaneAbove

WorkspaceView::focusPaneBelow

WorkspaceView::focusPaneOnLeft

WorkspaceView::focusPaneOnRight

WorkspaceView::focusPreviousPane

WorkspaceView::getActivePaneItem # This belongs on Workspace

WorkspaceView::getActivePane

WorkspaceView::getActiveView

WorkspaceView::getFocusedPane

WorkspaceView::indexOfPane

Workspace

Add

Workspace::getPanes

Workspace::getActivePane

Workspace::getActivePaneItem

Keep

Workspace::getEditors

Workspace::eachEditor

Workspace::getActiveEditor

Workspace::open

Workspace::registerOpener

Workspace::unregisterOpener

Deprecate or Remove

Workspace::destroyActivePane # This should be Pane::destroy() or Pane::close()

Workspace::saveActivePaneItem

Workspace::saveActivePaneItemAs

Workspace::reopenItemSync

Workspace::destroyActivePaneItem

Issue 2:
Not sure how to describe this or what actually caused it. After hitting cmd+z a few times, the debugger opened and code started duplicating in my file strangely. I restarted atom and tried to open the folder again, but the window stays white and I get this in the console:

TypeError: Cannot call method 'addMarkerAtLevel' of undefined
at IntervalSkipList.module.exports.IntervalSkipList.placeMarker (/Applications/Atom.app/Contents/Resources/app/node_modules/telepath/node_modules/interval-skip-list/lib/interval-skip-list.js:309:14)
at IntervalSkipList.module.exports.IntervalSkipList.insert (/Applications/Atom.app/Contents/Resources/app/node_modules/telepath/node_modules/interval-skip-list/lib/interval-skip-list.js:116:12)
at IntervalSkipList.module.exports.IntervalSkipList.update (/Applications/Atom.app/Contents/Resources/app/node_modules/telepath/node_modules/interval-skip-list/lib/interval-skip-list.js:140:19)
at ArrayMarker.module.exports.ArrayMarker.updateIndices (/Applications/Atom.app/Contents/Resources/app/node_modules/telepath/lib/array-marker.js:678:51)
at new ArrayMarker (/Applications/Atom.app/Contents/Resources/app/node_modules/telepath/lib/array-marker.js:44:12)
at Array.module.exports.Array.finalizeCreation (/Applications/Atom.app/Contents/Resources/app/node_modules/telepath/lib/array.js:79:30)
at Map.module.exports.Map.finalizeCreation (/Applications/Atom.app/Contents/Resources/app/node_modules/telepath/lib/map.js:54:15)
at Array.module.exports.Array.finalizeCreation (/Applications/Atom.app/Contents/Resources/app/node_modules/telepath/lib/array.js:97:15)
at Map.module.exports.Map.finalizeCreation (/Applications/Atom.app/Contents/Resources/app/node_modules/telepath/lib/map.js:54:15)
at Map.module.exports.Map.finalizeCreation (/Applications/Atom.app/Contents/Resources/app/node_modules/telepath/lib/map.js:54:15)
at Database.module.exports.Database.applyOperations (/Applications/Atom.app/Contents/Resources/app/node_modules/telepath/lib/database.js:282:18)
at Function.module.exports.Database.deserialize (/Applications/Atom.app/Contents/Resources/app/node_modules/telepath/lib/database.js:49:16)
at Function.module.exports.Document.deserialize (/Applications/Atom.app/Contents/Resources/app/node_modules/telepath/lib/document.js:48:32)
at Atom.module.exports.Atom.loadWindowState (/Applications/Atom.app/Contents/Resources/app/src/atom.js:472:24)
at Atom.module.exports.Atom.getWindowState (/Applications/Atom.app/Contents/Resources/app/src/atom.js:498:33)
at Atom.module.exports.Atom.initialize (/Applications/Atom.app/Contents/Resources/app/src/atom.js:93:73)
at Atom.module.exports.Atom.setUpEnvironment (/Applications/Atom.app/Contents/Resources/app/src/atom.js:98:19)
at Object.<anonymous> (/Applications/Atom.app/Contents/Resources/app/src/window-bootstrap.js:17:8)
at Object.<anonymous> (/Applications/Atom.app/Contents/Resources/app/src/window-bootstrap.js:25:4)
at Module._compile (module.js:471:26)
at Object.Module._extensions..js (module.js:489:10)
at Module.load (/Applications/Atom.app/Contents/Resources/app/node_modules/coffee-script/lib/coffee-script/coffee-script.js:211:36)
at Function.Module._load (module.js:327:12)
at Module.require (module.js:379:17)
at require (module.js:395:17)
at window.onload (file:///Applications/Atom.app/Contents/Resources/app/static/index.html:12:9) index.html:20
window.onload

I resolved the problem with this:

rm -fr ~/.atom/storage