Update project docs and metadata for new layout

Document the host/container split and update the package scripts and ignore rules to match the reorganized structure.

Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-opencode)

Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>

.gitignore

@@ -1,3 +1,4 @@
+host/state/
 state/
 .DS_Store
 node_modules/