fix: scope uninstall guidance cleanup

changes/scope-interactive-uninstall-guidance.fixed.md

@@ -0,0 +1,6 @@
+---
+"githits": patch
+"@githits/mcp": none
+---
+
+- **Respect uninstall selection for guidance** - Interactive user uninstall now removes guidance only for selected tools whose MCP is absent after cleanup and preserves shared guidance usable by any detected tool that was kept.

docs/implementation/cli-commands.md

@@ -140,9 +140,9 @@ Global setup supports Claude Code, Cursor, Windsurf, VS Code / Copilot, Cline, C
 
 The command uses `createContainer()` lazily for the login step. Tool detection and configuration use lightweight dependencies that don't require auth.
 
-The top-level `githits uninstall` command reverses the tool configuration performed by init; `githits init uninstall` remains a compatibility alias with the same flags and behavior. In interactive mode it first asks whether to remove user-level config or project-level config. User-level uninstall scans the same supported agents, removes only GitHits MCP/plugin entries, and leaves authentication credentials untouched. Unless `--keep-guidance` is passed, it also removes all four canonical GitHits skill files and the exact historical Cline/Junie `githits-mcp/SKILL.md` files, while preserving unrelated skills and directories. Use `githits logout` separately to remove stored credentials. For Claude Code, user-level inspection reads `$CLAUDE_CONFIG_DIR/.claude.json` when `CLAUDE_CONFIG_DIR` is non-empty, otherwise `~/.claude.json`; it inspects only `mcpServers.githits`, skips an already-absent removal, and rereads the structure after mutation. Malformed or unreadable Claude state blocks MCP mutation. Config-file uninstall removes `GitHits`/case-variant server entries while preserving other MCP servers and user settings; MCP host-config cleanup preserves the host config files and directories. Project uninstall uses the verified project config paths above, removes only GitHits entries from project-local files, preserves unrelated servers/settings, and best-effort removes legacy `.githits/init/project-setup.json` markers from earlier versions. Project uninstall does not remove global tools or Pi's global `pi-mcp-adapter` package because they can be shared by other projects; legacy, pre-existing, and GitHits-installed global Pi adapters are left installed. User-level Pi uninstall removes the `GitHits` entry from Pi's MCP config and runs `pi remove npm:pi-mcp-adapter` when the Pi CLI is available; if Pi is no longer installed, stale Pi MCP config entries are still removable without attempting adapter cleanup. Project uninstall is best-effort across supported config paths: missing files and files without GitHits are skipped, malformed/read-only/write-failing files are reported in the final summary, and the command exits 1 only after all possible removals have been attempted. JSONC-style files are accepted on read and rewritten as canonical JSON only when changed, matching setup behavior. Codex project setup rewrites `.codex/config.toml` as TOML and does not preserve existing TOML comments or formatting.
+The top-level `githits uninstall` command reverses the tool configuration performed by init; `githits init uninstall` remains a compatibility alias with the same flags and behavior. In interactive mode it first asks whether to remove user-level config or project-level config. User-level uninstall scans the same supported agents, removes only GitHits MCP/plugin entries, and leaves authentication credentials untouched. Unless `--keep-guidance` is passed, interactive user uninstall also removes the four canonical GitHits skill files and exact historical Cline/Junie `githits-mcp/SKILL.md` files owned by the selected tools. Guidance usable by an unselected detected tool is retained, including shared targets, and a selected tool retains its guidance when its MCP removal fails. Non-interactive `--yes` and user uninstall with no configured MCP target clean every verified user guidance target; project uninstall cleans every verified project guidance target. Unrelated skills and directories are preserved. Use `githits logout` separately to remove stored credentials. For Claude Code, user-level inspection reads `$CLAUDE_CONFIG_DIR/.claude.json` when `CLAUDE_CONFIG_DIR` is non-empty, otherwise `~/.claude.json`; it inspects only `mcpServers.githits`, skips an already-absent removal, and rereads the structure after mutation. Malformed or unreadable Claude state blocks MCP mutation. Config-file uninstall removes `GitHits`/case-variant server entries while preserving other MCP servers and user settings; MCP host-config cleanup preserves the host config files and directories. Project uninstall uses the verified project config paths above, removes only GitHits entries from project-local files, preserves unrelated servers/settings, and best-effort removes legacy `.githits/init/project-setup.json` markers from earlier versions. Project uninstall does not remove global tools or Pi's global `pi-mcp-adapter` package because they can be shared by other projects; legacy, pre-existing, and GitHits-installed global Pi adapters are left installed. User-level Pi uninstall removes the `GitHits` entry from Pi's MCP config and runs `pi remove npm:pi-mcp-adapter` when the Pi CLI is available; if Pi is no longer installed, stale Pi MCP config entries are still removable without attempting adapter cleanup. Project uninstall is best-effort across supported config paths: missing files and files without GitHits are skipped, malformed/read-only/write-failing files are reported in the final summary, and the command exits 1 only after all possible removals have been attempted. JSONC-style files are accepted on read and rewritten as canonical JSON only when changed, matching setup behavior. Codex project setup rewrites `.codex/config.toml` as TOML and does not preserve existing TOML comments or formatting.
 
-Unless `--keep-guidance` is passed, global guidance cleanup attempts every verified skill and managed-block target independently. Already-absent targets are quiet, supported skill-directory symlinks remain in place after `SKILL.md` removal, and hard failures keep their target path while later targets continue. Guidance is rendered separately from MCP agents: changed or failed paths are shown, all-absent guidance collapses to one unchanged row, guidance affects the headline and exit status, and agent counts exclude it.
+Guidance cleanup attempts each in-scope skill and managed-block target independently. Already-absent targets are quiet, supported skill-directory symlinks remain in place after `SKILL.md` removal, and hard failures keep their target path while later targets continue. Guidance is rendered separately from MCP agents: changed or failed paths are shown, protected targets collapse to one unchanged row stating how many targets tools may still use, all-absent guidance collapses to one unchanged row, guidance affects the headline and exit status, and agent counts exclude it.
 
 For automation, `githits uninstall --yes` is user-level only and never touches project files. Use `githits uninstall --project --yes` for non-interactive project-level removal. The nested `githits init uninstall` form remains supported for compatibility.
 

docs/implementation/init-guidance-and-expanded-agent-support.md

@@ -106,12 +106,17 @@ After successful cleanup, another guided run is a no-op for that migration.
 
 The canonical command is `githits uninstall`; `githits init uninstall` remains
 a compatibility alias with identical `--yes`, `--project`, and
-`--keep-guidance` behavior. Without `--keep-guidance`, uninstall independently
-and best-effort removes all four active skill files and the exact historical
-Cline/Junie files for the chosen scope, while preserving unrelated files and
-directories. Removing a shared root can affect every compatible agent that
-reads that directory; the result reports the shared guidance target. The
-`--keep-guidance` option preserves active and historical guidance.
+`--keep-guidance` behavior. Without `--keep-guidance`, interactive user
+uninstall best-effort removes active and historical guidance only for selected
+tools. It retains a shared skill or managed-block target when any unselected
+detected tool could use it, and retains a selected tool's guidance when its MCP
+removal fails. Non-interactive `--yes`, project uninstall, and user uninstall
+with no configured MCP targets clean every verified guidance target in the
+chosen scope. Cleanup removes all four active skill files and the exact
+historical Cline/Junie files while preserving unrelated files and directories.
+The `--keep-guidance` option preserves active and historical guidance.
+When cleanup removes a shared root, the result warns that every compatible
+agent reading that root is affected.
 
 Human output lists created, updated, unchanged, removed, and failed skill files
 accurately. Uninstall failure reasons are sanitized while failed target paths

docs/implementation/init-setup-output.md

@@ -64,13 +64,20 @@ preselected, the user deselects tools to retain, and the selection is the
 consent. `--yes` removes all configured user-level MCP targets. Project
 uninstall deduplicates project config paths and uses one confirmation.
 
-Without `--keep-guidance`, uninstall independently and best-effort removes all
-four active skill files at verified roots plus only the historical CLI-owned
-files `<scope>/.cline/skills/githits-mcp/SKILL.md` and
-`<scope>/.junie/skills/githits-mcp/SKILL.md`. It preserves unrelated skills,
-directories, plugin payloads, and credentials. Removing a shared root can
-affect every compatible agent that reads that directory. `--keep-guidance`
-preserves both active and historical guidance.
+Without `--keep-guidance`, interactive user uninstall best-effort removes the
+active and historical guidance targets owned by the selected tools. Guidance
+usable by any unselected detected tool is retained, including a shared skill or
+managed-block target also used by a selected tool. A selected tool also retains
+its guidance when its MCP removal fails. Non-interactive `--yes`,
+project uninstall, and user uninstall with no configured MCP targets continue
+to clean every verified guidance target in their chosen scope. Cleanup removes
+all four active skill files plus only the historical CLI-owned files
+`<scope>/.cline/skills/githits-mcp/SKILL.md` and
+`<scope>/.junie/skills/githits-mcp/SKILL.md`; it preserves unrelated skills,
+directories, plugin payloads, and credentials. `--keep-guidance` preserves both
+active and historical guidance. When cleanup removes a shared skill
+root, the output warns that every compatible agent reading that root is
+affected.
 
 Missing files are successful no-ops. A historical Cline or Junie file is
 removed only after a complete active shared skill set has been written and