refactor(config): decouple manifest path selection

[hongjr03]

Summary

• Split TOML manifest parsing from resolved workspace path selection.
• Move source/include/exclude path selection into project-model.
• Let vfs track included files and source files through a generic PathSelection / FileSetFilter.
• Let base-db classify source files from final FileIds instead of manifest path rules.

Notes

This keeps the existing manifest path semantics. Glob/gitignore behavior is intentionally not included in this PR.

Validation

• cargo check -p project-model -p vfs -p base-db -p vfs-notify
• cargo test -p project-model -p vfs -p base-db
• cargo test -p vizsla manifest
• cargo xtask check-manifest-schema
• npm test in editors/vscode

Prepare for #58.