Atlas Setup

Read the dependency registry and the bundled stack snapshot. For the current selection, use a manifest supplied by the user; otherwise use stacks/atlas.json when working in the Atlas repository, or fetch https://atlas.logbookfordevs.com/stack.json. If the current manifest is unavailable, use the bundled snapshot and disclose that freshness could not be verified. Retain the selected manifest's source and revision or fetch time for the comparison.

Check which selected Atlas packages and independent skills are available to the current host. Use the host's inventory and Skills CLI's installed-skill listing when needed. Match source and skill identity, not name alone, and distinguish missing skills from installed copies that are disabled or inaccessible to this host. Establish project/global scope and target agents before proposing filesystem changes.

Missing skills

For installed Atlas packages, collect missing dependencies from the registry and combine repeated entries. Show each upstream source, the affected skill and condition, whether it is required for that path or optional, and its installation command. Exclude dependencies of Atlas packages the user has not installed. If package discovery is unavailable, ask which Atlas skills to prepare.

Also show missing selections from the chosen stack as recommended additions, separate from required dependencies. A selected subset is valid; do not describe the entire stack as mandatory.

Ask which additions the user wants. Provide Skills CLI commands for the selected source and skill. Run installation only when authorized, using the chosen scope and agents; consult CLI help for supported options. Verify availability afterward and report activation or session-refresh gaps. If nothing is missing, say so without reinstalling.

Cleanup

Compare installed sources and previous Atlas selections with the chosen stack. When formerly selected, replaced or duplicate installations are found, read Cleanup and present a removal proposal. Skills outside the stack may be intentional independent installations; absence alone never establishes that they are obsolete.

Run removals only after the user explicitly approves the concrete targets and scope. Checking setup or approving additions does not authorize removal. Report additions, retained extras, approved removals and unresolved gaps separately.