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auto_update_manifest appends its YAML fragment to the end of the file, so a new entry joins whichever section happens to be last rather than tools. In this repo that is `environment`, so every auto-discovered command was filed under the wrong category in --help. The code says "indent the fragment to sit under the tools: key" and then does not do it. The dedup check reads only `tools`, so an entry parked in another section is not seen as taken and gets written a second time. YAML keeps both keys and the later one silently wins. That is where the duplicate prune:static in the manifest came from. Entries are now spliced at the end of the tools section, and a name counts as taken when any section declares it. Co-authored-by: Hanzo Dev <[email protected]>