Reorganize the installed filesystem and clean /bin

[frankischilling]

Part of #13

What to build

Reorganize the installed Cupid OS filesystem now that programs are built with Cupid tooling. /bin may remain, but it should contain only executable programs that belong in a conventional command directory. Programs such as Cupid Shell, Paint, and other applications or commands launched by users should remain in /bin when that is their proper installed location. Move supporting files into existing or newly created directories that match their purpose.

Inventory every file currently installed under /bin and classify it before moving or removing anything. Create or reuse suitable locations for libraries, internal toolchain files, demos, assets, Doom data, configuration, user documents, generated content, and other non-command files. Update every path consumer so programs continue to work from their new locations.

Acceptance criteria

• Record every installed /bin entry, its purpose, its producer, and its destination.
• Keep executable user programs and system commands that properly belong in /bin, including Cupid Shell, Paint, and similar installed applications.
• Do not move a program out of /bin merely because self-hosting allows it to be placed elsewhere; choose locations from the program's role in the installed system.
• Create or reuse clear filesystem directories for libraries, assets, data, configuration, documents, demos, and internal tooling.
• Move non-command supporting files to those directories and remove files that are proven redundant.
• Update build installation tables, launch paths, shell lookup, application shortcuts, tests, documentation, and runtime consumers.
• Preserve compatibility where a public path must remain stable, with an explicit alias or migration rule rather than a duplicate file.
• Verify filesystem listing, program launch, editor/notepad behavior, Doom assets, user programs, and a normal boot from the reorganized image.
• Document the final filesystem layout in the wiki, README where appropriate, and CTXT manuals.

Blocked by

• Bootstrap Cupid OS with a self-hosting Cupid toolchain #13

This work starts after the self-hosting bootstrap is complete and must finish before the bootstrap branch merges to main.