Module Structure ideas

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Hello List,

Last year I began to sepearte my module files to many files for their 
purposes.

Last time use use lots of dirs for their types

someting like

controllers
  a.cont.php
  b.cont.php
definition
  a.def.php
  b.def.php
models
  a.model.php
  b.model.php
views
  a.view.php
  b.view.php

Then I realize this model creates confusion when you start to debug a module.

My next step was putting module files in one dir, 
also I want to load them into text editor with spesific order 
(same to including order).

and I came up some ting like this

a.test.def.php
c.test.mdl.php
e.test.cnt.php
g.test.rtr.php
i.test.view.php
k.test.dr.js
m.test.m.js
o.test.css

test_app.a.def.php
test_app.c.mdl.php
test_app.e.cnt.php
test_app.g.rtr.php
test_app.i.view.php
test_app.k.dr.js
test_app.m.js
test_app.o.css

test.adef.php
test.cmdl.php
test.ecnt.php
test.grtr.php
test.iview.php
test.kdr.js
test.m.js
test.o.css

My point of view the 3. option is good for me.  

So I want to ask  this 

(beacause I'm using very closed working model. Just KDE and KATE)

is kind of file structure may lead any kind of problems in future or 
diffrerent situation ?

also is there any suggestion to using different methot to archive similar 
goals.

Regards

Sancar

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