Remove todo notes from documentation

Last remaining relevant todo notes have been filed as issues in GitLab.

doc/index.rst

@@ -44,7 +44,7 @@ Additional notes
    :maxdepth: 2
 
    development
-   todo
+   issues
    new-organism
    changelog
    copyright

doc/issues.rst

+Issues
+======
+
+For historical reasons, we currently have two issue trackers:
+
+1. `Mutalyzer Trac -- Active tickets
+   <https://humgenprojects.lumc.nl/trac/mutalyzer/report/2>`_
+2. `Mutalyzer GitLab -- Open issues
+   <https://git.lumc.nl/mutalyzer/mutalyzer/issues>`_
+
+The first, on the Mutalyzer Trac website, is the advertised location for end
+users to report issues. This is also where most feature requests are tracked.
+
+The second, on the Mutalyzer GitLab project site, is mainly for
+developers. Most issues here are of infrastructural or technical nature.
+
+In addition to these issue lists, smaller and more specific notes can be found
+by grepping the source code for ``Todo``.

doc/todo.rst

-Todo list
-=========
-
-These are some general todo notes. More specific notes can be found by
-grepping the source code for ``Todo``.
-
-.. seealso::
-
-   `Mutalyzer Trac -- Active tickets <https://humgenprojects.lumc.nl/trac/mutalyzer/report/2>`_
-     Users can file tickets on the Mutalyzer Trac website.
-
-   `Mutalyzer GitLab -- Open issues <https://git.lumc.nl/mutalyzer/mutalyzer/issues>`_
-     Some issues are recorded in the Mutalyzer GitLab project.
-
-- Improve the web interface design :)
-- Test all uses of mkstemp().
-- Use naming conventions for modules Crossmap, Db, File, GenRecord, Retriever
-  and Scheduler.
-- Use standard logging module, with rotating functionality. Race conditions
-  on the log file are probably a problem in the current setup.
-  Instead of that rotating, we could also use logrotate:
-  http://serverfault.com/questions/55610/logrotate-and-open-files
-- Setup continuous integration. Currently, I'm most impressed with Hudson.
-  - http://hudson-ci.org/
-  - http://www.rhonabwy.com/wp/2009/11/04/setting-up-a-python-ci-server-with-hudson/
-  Or perhaps Jenkins.
-  - http://jenkins-ci.org/
-- Migrate Javascript to JQuery.
-- I think in the long run, the Output object is not really the way to go. It
-  obscures the control flow. The logging part should use the standard logging
-  module. The data gathering by the Output object is probably better handled
-  by explicitely returning data objects from functions.
-- Check for os.path.join vulnerabilities.
-- There are some problems with the batch architecture, especially that there
-  cannot be multiple workers without synchronisation problems.
-  Good read: http://news.ycombinator.com/item?id=3002861
-  Suggestion: http://celeryproject.org/
-- Be more explicit in all the type of descriptions we don't currently
-  support.