README.DEVELOPER

  Refactoring TODO
  ================

1) Separate logic (decouple code) by packing into 

    caps.visual  - all the GUI related primitives. Should be intepended from
                   main computational cycles (algorithms), which run in
                   parrallel (hence must be as lightweight as possible).

    caps.debug   - functions for verbosity output.

    caps.results - function to read input parameters (of models) and save
                   intermidiate and final results at all stages of simulation.

    caps.config  - create a separate namespace for several parameters.

2) Continue fixing/correcting side-effects of earlier refactoring efforts, 
   e.g. getting of global variable space (too many global variables problem 
   - which results in high code coupling).
   Reduce number of parameters in all functions (not more than 5 
   input/output parameters are to be allowed) [use "handles" to structure 
   variables - collection of groups of variables]. 

3) Move out faculty/secondary code like analysis and plotting of data into
   tools/* folder of CAPS.

4) Rewrite all code comments. Each commented section should be a separate 
   (new) file or function. Each script or function should start with 
   correct MATLAB documentation headaer according to special format supported 
   by MATLAB (should follow code-to-documentation mechanism)

5) Add and create contents.m code (see other toolboxes and SimuCell).

x) Reduce the length of any program element (files, functions, etc.), i.e.
   reduce number of lines by making more files