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install.sh always overwrites deployed files
install.sh overwrites ~/.claude/ and ~/.claude/core/ unconditionally on every run. It does not merge, diff, or ask. The rationale: the source of truth is this repo. Editing deployed files directly is a usage error — sync.sh would overwrite those edits on the next pull anyway. Offering a merge path would imply that editing ~/.claude/CLAUDE.md directly is a supported workflow, which it is not. If a local customisation is needed it belongs in a project-level override file, not in the deployed global config.
Exception — skills: ~/.agents/skills/ uses a merge-per-skill strategy. Each skill directory from .agents/skills/ is replaced individually; the parent directory is never wiped. This preserves user-installed skills from other sources alongside the skills managed by this repo. The overwrite-always principle still holds for each individual managed skill — the per-skill replace is unconditional.