Minor changes (doxygen version and imports)
Changed file headers

Added URL to development branch in github and trimmed lines.
Improve code readability (1)

This commit includes the following improvements:
- improve order of fields and calls in methods (MainFrame,
  InternalFrameFactory)
- inline variables that were only used once (CommandStartExecuting,
  CommandRunFromEditor, InternalFrameFactory)
- use extended `for` loop if index is not used (CommandResetSimulator)
- use `return <bool expr>` instead of an `if` statement checking the state of
  the boolean expression (MainFrame)
- remove unnecessary blank lines, trim trailing white space
Improve code readability (2)

This commit includes the following improvements:
- inline variables that were only used once
- use extended `for` loop if index is not used
- remove unnecessary blank lines, trim trailing white space
- remove unnecessary and collapse empty curly braces
Improve code readability (3)

This commit includes the following kinds of improvements:
- inline variables that were only used once where it improves readability
- use extended for-loop is index is not used/required
- add access modifiers to fields where appropriate, reorder some fields
- strip trailing whitespace, remove unneeded empty lines, add line-breaks to
  very long lines
- move additional condition to loop head instead of using `break` inside the
  loop
- add `final` modifier to some local variables where appropriate