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-a can be used to add a folder to an existing window
Multiple folders can be added to the side bar. Using the Project/Add Folder to Project menu item is one way to do this
The command line is working as intended with respect to folders and new windows in the current dev builds (unwarranted empty windows are no longer created)
Ctrl+Tab does this
You can hide the side bar from the view menu
Thanks for providing the detailed followup information.

Sublime Text provides a natural way to edit multiple lines simultaneously: select the lines of interest, then use the "Selection/Split Selection into Lines" menu item to get one selection per line.

Once you have per-line selections, you can easily make batch edits modifying each line, without requiring a separate dialog.
Please provide more details for suggestions, this doesn't give much to go off
Take a look at ~/.config/sublime-text-2/Packages/Default/Icon.png
Unchecking the 'Highlight Matches' button on the find panel will speed things up
Both Cmd+Y and Cmd+Shift+Z will perform a redo