Several doc pages under Running TARDIS section are missing from TOC

[jaladh-singhal]

There are several helpful doc pages in TARDIS documentation which do appear on keyword searching the docs but not in TOC which is expected way of accessing.

1. In Interacting with TARDIS section of tardis docs, there is no TOC defined. Thus a docs user can't access the contents (notebooks and rst files) that are actually present in this section.

2. Similarly in Running TARDIS section, the to_hdf.rst and using_formal_integral.rst are not listed in TOC despite they are present in source.

3. Storing simulations to HDF page page (which is not yet listed in TOC as mentioned in point 2) have incorrect linking to the notebooks which are actually present in interaction directory with same name.

Some Pointers

• There maybe several other pages which are not yet listed (or listed incorrectly) in TARDIS docs, it'll be better if we get them fixed.
• Last time I locally build Sphinx docs, it threw lot of warnings about things that are present in source but not listed in any toc of that directory - those warnings can be great starting point to figure out where linking is wrong or missing.