Add an emitChanged method to QtGui::Molecule.

This allows users of the reference methods to indicate that the
molecule has changed.

Change-Id: Ie764155bd82752ef50e0fc4d5f76370c3d9d9f8f
Use a temporary OBProcess for querying read formats.

This is necessary for later changes, which call other query
methods in QtPlugin::OpenBabel that would clash if they shared
the same process.

Also make the handleReadFormatUpdate argument const& and make a
trivial organizational change in OBProcess::readFile.

Change-Id: I439116eefddf7b3683f7410567a9739a7accf02c
Expose obabel --minimize in the OpenBabel extension.

Pop up a configuration gui, start the minimization, show
step and energy info in a progress bar, and load the molecule
when finished.

Change-Id: Iaffdd581425e8e356caf33546c4f3e20a4ecf29c
Merge remote-tracking branch 'origin/master' into 116-OpenBabelForceFields

Conflicts:
	avogadro/qtplugins/openbabel/obprocess.cpp

Change-Id: I14b9fbf0cf416f5acf24ecb84c1845e3015610e8
Fix issues in previous commit.

* Move geometry optimization actions to Extensions menu
* Rename "default" forcefield to "recommended"/"autodetect"
* Split optimization configuration from optimization operation
* Fix tab order in OBForceFieldDialog
* Add shortcut (Ctrl+Alt+O) for geometry optimization
* Change action text to put (Open Babel) in parenthesis.

Change-Id: Ifb59cbfda72947f7f444ea57369a444918689ec5
Merge topic '116-OpenBabelForceFields' into master

950325e5 Fix issues in previous commit.
a12daf4d Merge remote-tracking branch 'origin/master' into 116-OpenBabelForceFields
e16606e4 Expose obabel --minimize in the OpenBabel extension.
44040e85 Use a temporary OBProcess for querying read formats.
ce9d8848 Add an emitChanged method to QtGui::Molecule.