setup: Replace directory-level install with per-asset merge-aware install - #180
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…tall sce setup previously staged the full catalog into a temp directory and swapped it over the whole .claude/, .opencode/, or .pi/ target directory, destroying any user-owned files (skills, settings.local.json, CLAUDE.md, etc.) living alongside SCE's own assets. The two generated JSON configs (.claude/settings.json, .opencode/opencode.json) had the same problem one level down: written whole, they clobbered a user's permissions, env, model, mcp, or non-SCE hook/plugin entries. Installation now happens per asset: each embedded file is staged and atomically renamed into place individually, and assets the current selection or catalog no longer owns are pruned by relative path instead of the whole directory being rebuilt. The two config files are merged via a new config_merge module that replaces only the SCE-owned fragment (hook entries by marker, plugin paths by prefix) and leaves every other key and entry untouched, idempotently across repeated installs. sce doctor's integration inspection is updated to match: the two merge-target configs are checked by whether their SCE-owned fragment is current rather than by byte-exact sha256, and `--fix` gained a repair path that reinstalls just a drifted merge-target asset. Co-authored-by: SCE <sce@crocoder.dev>
…iting them Every setup write — config assets and required git hooks alike — unlinked the destination file before renaming the staged replacement over it. The staging file already lives in the destination's directory, so the rename alone is atomic; the unlink only opened a window where the file did not exist, and on a rename failure the error path deleted the staging copy too, leaving neither. This mattered once `.claude/settings.json` and `.opencode/opencode.json` became merge targets holding user-owned keys that setup cannot reconstruct. Both pre-deletes are dropped in favor of atomic rename. `sce setup --hooks` also replaced `pre-commit`, `commit-msg`, and `post-commit` wholesale, destroying any hook a repository already ran (husky, lefthook, hand-written). Each canonical hook payload is now delimited by an SCE managed block marker pair. Install creates the full script when no hook exists, replaces the block in place when one already carries it, recognizes and replaces a legacy pre-marker SCE payload wholesale, and otherwise appends the block after a foreign hook's content so SCE always runs last. A last-effective-line heuristic reports an advisory when a foreign hook's trailing zero-indent `exec`/`exit` would make the appended block unreachable. `sce doctor` now classifies hook content by managed-block currency instead of byte-exact comparison, so foreign content around a current block does not read as drift. Co-authored-by: SCE <sce@crocoder.dev>
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