I think this data structure could be improved on a bit. Here's my suggestion:
```python
from collections import namedtuple
Page = namedtuple('Page', 'name title objects')

pages = [Page('importing', 'Importing Phase Objects', 
         ['@Solution', '@Mixture']),
         Page('thermodynamics', 'Thermodynamic Properties', ['@ThermoPhase']),
         Page('kinetics', 'Chemical Kinetics', ['@Kinetics']),
         Page('transport', 'Transport Properties', ['@Transport'])
         Page('zero-dim', 'Zero-Dimensional Reactor Networks', 
              ['@Func', '@Reactor', '@ReactorNet', '@FlowDevice', '@Wall']),
         Page('one-dim': 'One-Dimensional Reacting Flows', 
              ['1D/@Domain1D', '1D/@Stack'])
         Page('data', 'Built-In Thermochemical Data',
              ['air.m', 'constants.m', 'gasconstant.m', 'GRI30.m', 'Hydrogen.m',
               'Methane.m', 'Nitrogen.m', 'oneatm.m', 'Oxygen.m', 'Water.m']),
         Page('utilities', 'Utility Functions',
              ['adddir.m', 'ck2cti.m', 'cleanup.m', 'geterr.m', '@XML_Node']),
         Page('interface', 'Interfaces', ['@Interface'])
         ]

extra = {'@Solution': ('IdealGasMix.m', 'importPhase.m'),
         '@Func': ('gaussian.m', 'polynom.m'),
         '@Reactor': ('conhp.m', 'ConstPressureReactor.m', 'conuv.m',
                      'FlowReactor.m', 'IdealGasConstPressureReactor.m',
                      'IdealGasReactor.m', 'reactor_ode.m', 'Reservoir.m'),
         '@FlowDevice': ('MassFlowController.m', 'Valve.m'),
         '@1D/Domain1D': ('1D/AxiStagnFlow.m', '1D/AxisymmetricFlow.m',
                          '1D/Inlet.m', '1D/Outlet.m', '1D/OutletRes.m',
                          '1D/Surface.m', '1D/SymmPlane.m'),
         '@1D/Stack': ('1D/FreeFlame.m', '1D/npflame_init.m'),
         '@Interface': ('importEdge.m', 'importInterface.m')}

for page in pages:
    ...
    for obj in page.objects:
        if obj.endswith('.m'):
            # do things with individual files
        else:
            # do things for a class
            for item in extra.get(obj, ()):
                # do things for extra files associated with this class
```

This gives you more control over the order that things are presented, and the `namedtuple` and auxiliary data structure help get rid of the confusing indexing.