feat: fix skill transformation pipeline across all targets (#334)

plugins/compound-engineering/skills/ce-plan-beta/SKILL.md

@@ -145,12 +145,13 @@ Prepare a concise planning context summary (a paragraph or two) to pass as input
 
 Run these agents in parallel:
 
-- Task compound-engineering:research:repo-research-analyst(planning context summary)
+- Task compound-engineering:research:repo-research-analyst(Scope: technology, architecture, patterns. {planning context summary})
 - Task compound-engineering:research:learnings-researcher(planning context summary)
 
 Collect:
-- Existing patterns and conventions to follow
-- Relevant files, modules, and tests
+- Technology stack and versions (used in section 1.2 to make sharper external research decisions)
+- Architectural patterns and conventions to follow
+- Implementation patterns, relevant files, modules, and tests
 - AGENTS.md guidance that materially affects the plan, with CLAUDE.md used only as compatibility fallback when present
 - Institutional learnings from `docs/solutions/`
 

plugins/compound-engineering/skills/ce-plan/SKILL.md

@@ -83,11 +83,11 @@ First, I need to understand the project's conventions, existing patterns, and an
 
 Run these agents **in parallel** to gather local context:
 
-- Task compound-engineering:research:repo-research-analyst(feature_description)
+- Task compound-engineering:research:repo-research-analyst(Scope: technology, architecture, patterns. {feature_description})
 - Task compound-engineering:research:learnings-researcher(feature_description)
 
 **What to look for:**
-- **Repo research:** existing patterns, AGENTS.md guidance, technology familiarity, pattern consistency
+- **Repo research:** technology stack and versions (informs research decisions), architectural patterns, and implementation patterns relevant to the feature
 - **Learnings:** documented solutions in `docs/solutions/` that might apply (gotchas, patterns, lessons learned)
 
 These findings inform the next step.

plugins/compound-engineering/skills/deepen-plan-beta/SKILL.md

@@ -209,7 +209,7 @@ Use fully-qualified agent names inside Task calls.
 
 **Requirements Trace / Open Questions classification**
 - `compound-engineering:workflow:spec-flow-analyzer` for missing user flows, edge cases, and handoff gaps
-- `compound-engineering:research:repo-research-analyst` for repo-grounded patterns, conventions, and implementation reality checks
+- `compound-engineering:research:repo-research-analyst` (Scope: `architecture, patterns`) for repo-grounded patterns, conventions, and implementation reality checks
 
 **Context & Research / Sources & References gaps**
 - `compound-engineering:research:learnings-researcher` for institutional knowledge and past solved problems
@@ -223,11 +223,11 @@ Use fully-qualified agent names inside Task calls.
 
 **High-Level Technical Design**
 - `compound-engineering:review:architecture-strategist` for validating that the technical design accurately represents the intended approach and identifying gaps
-- `compound-engineering:research:repo-research-analyst` for grounding the technical design in existing repo patterns and conventions
+- `compound-engineering:research:repo-research-analyst` (Scope: `architecture, patterns`) for grounding the technical design in existing repo patterns and conventions
 - Add `compound-engineering:research:best-practices-researcher` when the technical design involves a DSL, API surface, or pattern that benefits from external validation
 
 **Implementation Units / Verification**
-- `compound-engineering:research:repo-research-analyst` for concrete file targets, patterns to follow, and repo-specific sequencing clues
+- `compound-engineering:research:repo-research-analyst` (Scope: `patterns`) for concrete file targets, patterns to follow, and repo-specific sequencing clues
 - `compound-engineering:review:pattern-recognition-specialist` for consistency, duplication risks, and alignment with existing patterns
 - Add `compound-engineering:workflow:spec-flow-analyzer` when sequencing depends on user flow or handoff completeness
 
@@ -249,6 +249,7 @@ Use fully-qualified agent names inside Task calls.
 #### 3.2 Agent Prompt Shape
 
 For each selected section, pass:
+- The scope prefix from section 3.1 (e.g., `Scope: architecture, patterns.`) when the agent supports scoped invocation
 - A short plan summary
 - The exact section text
 - Why the section was selected, including which checklist triggers fired