What is the best way to organize files in a web project?

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First of all, a thousand excuses if this question does not fit the objectives of the site.

I want to create a "pack" of themes/skins for wordpress (maybe with some mu plugins), phpbb (or similar) and mediawiki (or not), but first I need to come up with the design. My question is in organizing git repository folders, what is the least gambiarresca and/or more Profisisonal way to organize!? I’m only using basic text editors (Notepad++ or Brackets), so no IDE.

The tree more or less I use is this:

.
+-- .gitignore
+-- layouts
|   +-- blog
|   |   +-- <template "estático" do blog, antes de passar para o formato do wordpress>
|   +-- wiki
|   |   +-- <template "estático" da wiki, antes de passar para o formato do mediawiki>
|   +-- forum
|   |   +-- <template "estático" do forum, antes de passar para o formato do phpbb>
+-- sistemas
|   +-- blog
|   |   +-- <pasta do tema>
|   |   +-- mu-plugins
|   |   |   +-- <plugins MU do wordpress>
|   +-- forum
|   |   +-- <pasta do template phpbb>
|   +-- siki
|   |   +-- <pasta da skin mediawiki>
+-- LICENSE.md
+-- README.md
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