refactor: simplify repository layout and remove unused assets

[tiammomo]

ModelPort's tracked repository root shrinks from 37 entries to 25. Files now live with their owning component while the root setup, Cargo, Docker, and Compose commands retain their existing entry points.

• Move community policies into .github/, project policies into docs/project/, the operations Agent into crates/, embedded catalogs/schemas into resources/, shared fixtures into tests/fixtures/, Zig wrappers into scripts/toolchain/, and the npm audit policy into dashboard/. Update build, release, Compose, Rust include paths, and documentation links together; add the repository map to the development guide.
• Rebuild stale local executables when workspace code, embedded resources, or migrations change. Eight script regression cases cover reuse, modification, removal, and incomplete inputs; the original helper fails six of them.
• Remove the unreferenced 1.85 MiB legacy login illustration so it is no longer copied into every dashboard build.

Validation:

• scripts/check-all.sh passes: 475 Rust tests, 125 frontend tests, eight script regression tests, fmt/clippy, ShellCheck, documentation links, and configuration/adapter fixtures.
• Dashboard dependency audit reports zero vulnerability entries. Catalog/schema/fixture bytes and public schema IDs are unchanged.
• All three release-mode container builds pass from the clean commit, with matching source provenance labels. The local build uses a cached Rust 1.96.0 builder with the locked dependency registry.
• An isolated PostgreSQL Compose deployment passes gateway readiness, embedded schema validation, current login-image delivery, and two browser login tests. The legacy image is absent from the dashboard container; the optional Agent starts and passes readiness in disabled mode.
• All PR checks pass, including 21 PostgreSQL dashboard E2E cases, Rust/JavaScript CodeQL, and dependency review. No paid Provider calls.

Catalog/schema contents, public schema identifiers, package names, service names, and configuration contracts are preserved. This is a source-layout update; it does not create a new version tag or replace published 0.1.1 images.