doc: cleanup and make things more consistent.

The breadcrumbs now correctly indicate the module hierarchy and can be
used to determine imports. All the documentation for ost.* is now rooted
on the base `ost` module for more clarity.

modules/base/doc/base.rst

@@ -2,7 +2,22 @@
 ================================================================================
 
 .. toctree::
+  :maxdepth: 1
 
+  generic
   logging
+  ../bindings/bindings
+  ../conop/conop
+  ../db/db
+  ../geom/geom
+  ../gfx/gfx
+  ../gui/gui
+  ../img/base/img
+  ../io/io
+  ../mol/base/mol
+  ../seq/base/seq
   settings
+  table
   testutils
+
+

modules/base/doc/settings.rst

-:mod:`ost.settings` - Locate Files and Retrieve Preferences
+:mod:`~ost.settings` - Locate Files and Retrieve Preferences
 ================================================================================
 
 .. automodule:: ost.settings

modules/conop/doc/cleanup.rst

-:mod:`conop.cleanup <ost.conop.cleanup>` -- Sanitize structures
+:mod:`~ost.conop.cleanup>` -- Sanitize structures
 ================================================================================
 
 .. module:: ost.conop.cleanup

modules/db/doc/db.rst

-Linear Database
+:mod:`~ost.db` - Linear Database
 ===============================================================================
 
 .. currentmodule:: ost.db

modules/img/alg/doc/alg.rst

-:mod:`img.alg <ost.img.alg>` - Image Processing Algorithms
+:mod:`~ost.img.alg` - Image Processing Algorithms
 ================================================================================
 
 .. module:: ost.img.alg

modules/img/base/doc/img.rst

@@ -5,6 +5,7 @@
   :hidden:
 
   point-size-extent
+  ../alg/alg
 
 .. module:: ost.img
    :synopsis: Images and density maps

modules/index.rst

@@ -8,40 +8,10 @@ OpenStructure documentation
   install
   intro
   users
-  base/generic
   base/base
-  geom/geom
-  mol/base/mol
-  mol/alg/molalg
-  mol/alg/chain_mapping
-  mol/alg/contact_score
-  mol/alg/dockq
-  mol/alg/helix_kinks
-  mol/alg/ligand_scoring
-  mol/alg/qsscore
-  mol/alg/scoring
-  mol/alg/stereochemistry
-  mol/alg/structure_analysis
-  mol/alg/trajectory_analysis
-  mol/mm/molmm
-  conop/conop
-  img/base/img
-  img/alg/alg
-  seq/base/seq
-  seq/alg/seqalg
-  seq/alg/renumber
-  seq/alg/aaindex
-  db/db
-  bindings/bindings
-  io/io
-  gfx/gfx
-  gui/gui
   newmodule
   external
   contributing
-  table
-  mol/alg/lddt
-  mol/alg/molck
   actions
 
 For Starters
@@ -108,7 +78,7 @@ Graphical User Interface
 Varia
 --------------------------------------------------------------------------------
 
-**Datasets**: :doc:`tabular data <table>`
+**Datasets**: :doc:`tabular data <base/table>`
 
 **Supported File Formats**: :doc:`structure formats<io/structure_formats>` | :doc:`sequence formats <io/sequence_formats>` | :doc:`sequence profile formats <io/sequence_profile_formats>` | :doc:`image formats <io/image_formats>`
 

modules/mol/alg/doc/chain_mapping.rst

-:mod:`mol.alg.chain_mapping <ost.mol.alg.chain_mapping>` -- Chain Mapping
+:mod:`~ost.mol.alg.chain_mapping` -- Chain Mapping
 --------------------------------------------------------------------------------
 
 .. automodule:: ost.mol.alg.chain_mapping

modules/mol/alg/doc/contact_score.rst

-:mod:`mol.alg.contact_score <ost.mol.alg.contact_score>` -- Contact based scores
+:mod:`~ost.mol.alg.contact_score` -- Contact-Based Scores
 ------------------------------------------------------------------------------------
 
 .. automodule:: ost.mol.alg.contact_score
    :members:
    :member-order: bysource
-   :synopsis: Contact based scores
+   :synopsis: Contact-based scores

modules/mol/alg/doc/dockq.rst

-:mod:`mol.alg.dockq <ost.mol.alg.dockq>` -- DockQ implementation
+:mod:`~ost.mol.alg.dockq` -- DockQ Implementation
 --------------------------------------------------------------------------------
 
 .. module:: ost.mol.alg.dockq

modules/mol/alg/doc/helix_kinks.rst

-:mod:`mol.alg.helix_kinks <ost.mol.alg.helix_kinks>` -- Algorithms to calculate Helix Kinks
+:mod:`~ost.mol.alg.helix_kinks` -- Algorithms to Calculate Helix Kinks
 ---------------------------------------------------------------------------------------------------------------
 
 .. automodule:: ost.mol.alg.helix_kinks

modules/mol/alg/doc/lddt.rst

-====
-lDDT
-====
+:orphan:
+
+========================
+lDDT binary (deprecated)
+========================
 
 .. warning::
 

modules/mol/alg/doc/ligand_scoring.rst

-:mod:`mol.alg.ligand_scoring <ost.mol.alg.ligand_scoring>` -- Ligand scoring functions
+:mod:`~ost.mol.alg.ligand_scoring` -- Ligand scoring functions
 ------------------------------------------------------------------------------------------
 
 .. module:: ost.mol.alg.ligand_scoring

modules/mol/alg/doc/molalg.rst

-:mod:`mol.alg <ost.mol.alg>` -- Algorithms for Structures
+:mod:`~ost.mol.alg` -- Algorithms for Structures
 ================================================================================
 
 .. module:: ost.mol.alg
@@ -7,16 +7,19 @@
 Submodules
 --------------------------------------------------------------------------------
 
-* :doc:`chain_mapping – Chain Mapping <chain_mapping>`
-* :doc:`contact_score – Contact based scores<contact_score>`
-* :doc:`dockq – DockQ implementation<dockq>`
-* :doc:`helix_kinks – Algorithms to calculate Helix Kinks<helix_kinks>`
-* :doc:`ligand_scoring – Ligand scoring functions<ligand_scoring>`
-* :doc:`qsscore – New QS score implementation<qsscore>`
-* :doc:`scoring – Specialized scoring functions<scoring>`
-* :doc:`stereochemistry – Stereochemistry Checks<stereochemistry>`
-* :doc:`structure_analysis – Functions to analyze structures<structure_analysis>`
-* :doc:`trajectory_analysis – DRMSD, pairwise distances and more<trajectory_analysis>`
+.. toctree::
+  :maxdepth: 1
+
+  chain_mapping
+  contact_score
+  dockq
+  helix_kinks
+  ligand_scoring
+  qsscore
+  scoring
+  stereochemistry
+  structure_analysis
+  trajectory_analysis
 
 Local Distance Test scores (lDDT, DRMSD)
 --------------------------------------------------------------------------------
@@ -1451,4 +1454,3 @@ from a :class:`ost.io.MMCifInfoBioUnit` or the derived
   :param bu_info: Info object
   :type bu_info: :class:`MMCifInfoBioUnit`/:class:`BUInfo`
   :returns: A :class:`ost.mol.EntityHandle` of the requested biounit
-

modules/mol/alg/doc/molck.rst

+:orphan:
+
 ..  Note on large code blocks: keep max. width to 100 or it will look bad
                                on webpage!
 
-=========================
-Molecular Checker (Molck)
-=========================
+Molck - the Molecular Checker binary (deprecated)
+=================================================
 
 --------------------------------------
 Where can I find the Molck executable? 

modules/mol/alg/doc/qsscore.rst

-:mod:`mol.alg.qsscore <ost.mol.alg.qsscore>` -- New QS score implementation
+:mod:`~ost.mol.alg.qsscore` -- New QS Score Implementation
 --------------------------------------------------------------------------------
 
 .. note::

modules/mol/alg/doc/scoring.rst

-:mod:`mol.alg.scoring <ost.mol.alg.scoring>` -- Specialized scoring functions
+:mod:`~ost.mol.alg.scoring` -- Specialized Scoring Functions
 ---------------------------------------------------------------------------------
 
 .. module:: ost.mol.alg.scoring

modules/mol/alg/doc/stereochemistry.rst

-:mod:`mol.alg.stereochemistry <ost.mol.alg.stereochemistry>` -- Stereochemistry Checks
+:mod:`~ost.mol.alg.stereochemistry` -- Stereochemistry Checks
 --------------------------------------------------------------------------------------
 
 .. warning::

modules/mol/alg/doc/structure_analysis.rst

-:mod:`mol.alg.structure_analysis <ost.mol.alg.structure_analysis>` -- Functions to analyze structures
+:mod:`~ost.mol.alg.structure_analysis` -- Functions to Analyze Structures
 ---------------------------------------------------------------------------------------------------------------
 
 .. automodule:: ost.mol.alg.structure_analysis