Add python_titan and tools doc pages, fix example wording

[ercius]

Follow-up to the docs modernization merged in #87, which only included the first commit of the update-docs branch. This carries over the rest:

• Link python_titan properly in the Components toctree instead of as plain bold text (it needs a real docs/python_titan.rst target).
• Add docs/tools.rst and docs/python_titan.rst: docs/tools.rst had been deleted in a much older commit but the toctree entry pointing to it was never removed, so it silently failed to render on RTD.
• Reword the ncempy.read()/fileDM examples in docs/index.rst to use import ncempy directly instead of import ncempy.io as nio.