General layout:

assets directory: (root)
[js] misc, old
[css] standard.css
[media] fonts, [any general images needed for root pages E.G. Directory, copyright & licensing]

Each article within a Category Directory (Software, Writing, Music, Meta) is structured as follows:
/categoryName/articleName/index.html - the article content
/categoryName/articleName/assets/ - a directory of any assets the article references, good for keeping articles and their assets self-contained

Each Category Directory features its own index(.html) for indexing all articles:
/firstCategory/index.html
/secondCategory/index.html

Directory
[navbar] Search, About
[primary feature from any category]
[software feature(s)]
[writing feature(s)]
[music feature(s)]
[search box - linked to navbar Search button]
[footer] [Edit Date] copyright & licensing, Meta

META PAGES:

About
[navbar] Directory, More on Meta
[about info - intro, contact, etc]
[footer] [Creation & Edit Dates], "donations and things of that particular nature", copyright & licensing

Changelog
[navbar] Directory, See oldest, More on Meta
[changelog]
[footer] [Creation & Edit Dates], copyright & licensing

Contribute
[navbar] Directory, More on Meta
[contribute info - intro, donation options, etc.]
[footer] [Creation & Edit Dates], copyright & licensing

copyright & licensing (copyright at root of directory instead of /meta Category directory, for easy reference from other every page's footer)
[navbar] Directory, More on Meta]

CATEGORY PAGES: (index/Directory per Category)

Meta (More on Meta) [navbar] Directory, Changelog, Contribute, About
[meta intro, bullet list of links to Changelog, Contribute, About, copyright & licensing - links are phrased in F.A.Q. format]
[footer] [Creation & Edit Dates], copyright & licensing

Software
[navbar] Directory, About
[Latest in Software]
[Featured Article or Featured External Content]
[Previous Articles/Article Archive (T.B.D.)]
[Original Software Archive/Timeline]
[footer] [Creation & Edit Dates], copyright & licensing

Writing / Music / Any other category - same as above