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Add per-skill .version file and update instructions to llms.txt
Each skill zip (individual and fat) now contains a .version JSON file with
the commit SHA and ISO date of the last change to that skill's files, plus
zip_url and llms_txt back-references so an agent can discover update info
without prior knowledge of the registry.
manifest.json gains commit and date fields per skill for the same reason.
llms.txt gains a "Checking for and applying updates" section explaining the
comparison workflow (manifest commit vs. installed .version), and the install
section now mentions the .version file.
Version reflects per-skill git history, not publish time, so an unrelated
skill change does not mark all skills as modified.
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