chore: handle lightweight vs full plugin in shell file generation

agents/IMPLEMENTATION.md

@@ -56,6 +56,7 @@ For detailed change history, use git history and PRs instead of expanding this f
 ### Workflows and Automation
 
 - GitHub Actions were updated to remove most deprecated Node 20-era dependencies and align with newer action runtimes where upstream allowed it.
+- Init-workspace instructions now treat `rosetta@rosetta` as the MCP connector path rather than plugin mode, while any other plugin type is handled as plugin mode.
 - Workflow maintenance included:
   - Bun runtime override for Claude workflows
   - build/publish pipeline repairs

instructions/r2/core/skills/init-workspace-context/SKILL.md

@@ -18,11 +18,14 @@ Initialization must behave differently for fresh, existing, or plugin workspaces
 
 <core_concepts>
 - Rosetta prep steps completed
-- Three modes: install (no files per `bootstrap_rosetta_files`), upgrade (some files per `bootstrap_rosetta_files` exist), plugin (LLM context contains "Rosetta plugin is already active")
+- Three modes: install (no files per `bootstrap_rosetta_files`), upgrade (some files per `bootstrap_rosetta_files` exist), plugin (LLM context contains "RUNNING AS A PLUGIN" and plugin identifier other than "rosetta@rosetta")
+- `rosetta@rosetta` is not plugin mode; every other plugin type is treated as plugin mode
 </core_concepts>
 
 <process>
-1. Check LLM context for "Rosetta plugin is already active" — if found, set mode = plugin
+1. Check LLM context for "RUNNING AS A PLUGIN":
+   - If found AND context contains "rosetta@rosetta" → fall through to step 2 (not a plugin)
+   - If found and plugin type is anything else → set mode = plugin
 2. If not plugin, scan workspace for existing files per `bootstrap_rosetta_files`
 3. Any found → mode = upgrade; none → mode = install
 4. Scan for multiple sub-repositories with independent documentation roots → set composite flag, treat git repos as modules, requires use of `large-workspace-handling` skill

instructions/r2/core/workflows/init-workspace-flow-context.md

@@ -49,6 +49,7 @@ Determines workspace state before any changes occur. Without accurate mode detec
 
 <pitfalls>
 - Plugin mode is a context-sentence check, not filesystem detection
+- `rosetta@rosetta` is not a plugin; any other plugin type falls into plugin mode
 - Do not assume install if state file is fresh — files may exist on disk
 - Composite requires sub-repository docs, not just multiple directories
 </pitfalls>

instructions/r2/core/workflows/init-workspace-flow.md

@@ -26,9 +26,10 @@ Validation: State file tracks every phase with file inventory; verification conf
 - IF state.file_count >= 50 (set by Phase 3): pass "ACQUIRE `large-workspace-handling/SKILL.md` FROM KB" to Phase 5, 6, 8 subagents.
 - Before Phase 1: create `agents/init-workspace-flow-state.md`.
 - Conditional phases:
-  - If you have already in context "RUNNING AS A PLUGIN": MUST NOT EXECUTE "shells" phase 2 AND "rules" phase 4
+  - If you have already in context "RUNNING AS A PLUGIN" and plugin type is not `rosetta@rosetta`: MUST NOT EXECUTE "shells" phase 2 AND "rules" phase 4
   - Else if user explicitly requested to HAVE ALL RULES LOCALLY: MUST NOT EXECUTE "shells" phase 2, BUT MUST EXECUTE "rules" phase 4
   - Else MUST EXECUTE "shells" phase 2, BUT MUST NOT EXECUTE "rules" phase 4
+- Note: `rosetta@rosetta` is an MCP connector, not a plugin — it follows the normal path (shells phase 2 executes)
 - If user says to initialize rules, subagents, agents, workflows, commands it still means to execute "shells" phase 2.
 - Upgrade from R1 to R2 is exactly the same process as define here, but you already have some files available, which you can reuse.
 - Additionally tell subagents: "If you want to use shell commands, prefer to combine individual shell commands into single **simple** shell script in `agents/TEMP` and execute it, but already available tools ALWAYS take precedence."