feat(core): add replaces field to SkillDefinition for extension skill override

## Intent

When an extension contributes domain-specific skills (e.g. `sabdx-architecture`) that
supersede generic baseline skills provided by `codemcp-workflows-skilled` (e.g. `architecture`),
both sets were previously included in the resolved skills list — resulting in duplicate,
redundant skills shown at setup and installed into the project.

This change allows extension authors to declare which generic skills their domain skill
replaces, so the resolver can produce a clean, non-redundant final list.

## Key changes

- `InlineSkill` and `ExternalSkill` now accept an optional `replaces?: string[]` field
  listing the names of skills the declaring skill supersedes.
- The resolver post-processes the merged skills list: it collects all replaced names into
  a Set, deduplicates by name (last-writer-wins), then filters out any skill whose name
  appears in the replaced set. The result is the effective, non-redundant skills list.
- The `replaces` field is a resolver-level concern only — it is never written to SKILL.md
  frontmatter and does not appear in the lock file (which records the post-dedup list).
- With the sadb-agentic-template extension declaring `replaces` on all five lifecycle
  skills, the setup wizard reduces from 13 → 8 skills for the sabdx-frontend scenario.

## Dependencies and side effects

- The `replaces` field is purely additive — existing extension files without it continue
  to work unchanged.
- `writeInlineSkills()` in `util.ts` required no changes: it only reads `name`,
  `description`, and `body`, so `replaces` is silently ignored during file writing.

Author: mrsimpson

.beads/issues.jsonl

@@ -84,3 +84,14 @@
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.beads/last-touched

@@ -1 +1 @@
-ade-8.5
+ade-9.3.6

.vibe/beads-state-ade-extension-override-skills-d44z9p.json

@@ -0,0 +1,29 @@
+{
+  "conversationId": "ade-extension-override-skills-d44z9p",
+  "projectPath": "/Users/oliverjaegle/projects/privat/codemcp/ade",
+  "epicId": "ade-9",
+  "phaseTasks": [
+    {
+      "phaseId": "explore",
+      "phaseName": "Explore",
+      "taskId": "ade-9.1"
+    },
+    {
+      "phaseId": "plan",
+      "phaseName": "Plan",
+      "taskId": "ade-9.2"
+    },
+    {
+      "phaseId": "code",
+      "phaseName": "Code",
+      "taskId": "ade-9.3"
+    },
+    {
+      "phaseId": "commit",
+      "phaseName": "Commit",
+      "taskId": "ade-9.4"
+    }
+  ],
+  "createdAt": "2026-03-20T10:16:23.345Z",
+  "updatedAt": "2026-03-20T10:16:23.345Z"
+}

.vibe/development-plan-extension-override-skills.md

@@ -0,0 +1,110 @@
+# Development Plan: ade (extension-override-skills branch)
+
+*Generated on 2026-03-20 by Vibe Feature MCP*
+*Workflow: [epcc](https://mrsimpson.github.io/responsible-vibe-mcp/workflows/epcc)*
+
+## Goal
+Allow extension-contributed skills to declare that they replace/supersede generic baseline skills registered by the process option (`codemcp-workflows-skilled`). The resolver should deduplicate the final skills list so that only the effective (non-replaced) skills are shown and installed.
+
+## Explore
+<!-- beads-phase-id: ade-9.1 -->
+### Tasks
+- [x] Understand current skill registration flow (process → recipe → skills writer → LogicalConfig)
+- [x] Identify the exact duplication: `codemcp-workflows-skilled` registers 5 generic skills; architecture extensions like `sabdx-frontend` register domain-specific replacements with different names
+- [x] Evaluate solution options (replaces field, baseline priority, excludes at option level)
+- [x] Agree on preferred approach: `replaces?: string[]` on `SkillDefinition`
+
+### Phase Entrance Criteria:
+*(initial phase — no prior phase)*
+
+## Plan
+<!-- beads-phase-id: ade-9.2 -->
+### Tasks
+
+*Tasks managed via `bd` CLI*
+
+### Phase Entrance Criteria:
+- [ ] The problem is clearly understood: duplicate generic + domain-specific skills shown at setup
+- [ ] At least two solution alternatives have been evaluated
+- [ ] The preferred approach (`replaces` field on `SkillDefinition`) is agreed upon
+- [ ] Scope is clear: which files are touched
+
+## Code
+<!-- beads-phase-id: ade-9.3 -->
+### Tasks
+
+*Tasks managed via `bd` CLI*
+
+### Phase Entrance Criteria:
+- [ ] Concrete implementation plan is documented (what changes in which file)
+- [ ] Edge cases are identified (ordering, name-collision, TUI display)
+- [ ] Test strategy is defined
+
+## Commit
+<!-- beads-phase-id: ade-9.4 -->
+### Tasks
+- [ ] Squash WIP commits: `git reset --soft <first commit of this branch>`. Then, create a conventional commit. In the message, first summarize the intentions and key decisions from the development plan. Then, add a brief summary of the key changes and their side effects and dependencies.
+
+*Tasks managed via `bd` CLI*
+
+### Phase Entrance Criteria:
+- [ ] All implementation tasks are done and tests pass
+- [ ] The `replaces` field works end-to-end (resolver deduplicates, TUI shows reduced list)
+- [ ] No regressions in existing resolver tests
+
+## Key Decisions
+
+### KD-1: Add `replaces?: string[]` to `SkillDefinition`
+Both `InlineSkill` and `ExternalSkill` get an optional `replaces` field. Extension authors list the generic skill names they supersede. Deduplication happens as a post-processing step in the resolver (`resolve()` in `resolver.ts`).
+
+### KD-2: Deduplication strategy — last-writer-wins + replaces set
+After all provisions are merged, the resolver:
+1. Builds a Set of all names that appear in any skill's `replaces` array.
+2. Deduplicates by name (last occurrence wins, preserving insertion order otherwise) using a Map.
+3. Filters out any skill whose `name` is in the replaced-names Set.
+
+This means: if `sabdx-architecture` declares `replaces: ["architecture"]`, the generic `architecture` skill is dropped. The final list contains `sabdx-architecture` only.
+
+### KD-3: Skill file names on disk — unchanged
+Skills are written to `.ade/skills/<name>/SKILL.md` by `writeInlineSkills()` in `util.ts`.
+- The generic `architecture` skill → `.ade/skills/architecture/SKILL.md`
+- The replacing `sabdx-architecture` skill → `.ade/skills/sabdx-architecture/SKILL.md`
+
+Because `architecture` is filtered out **before** `writeInlineSkills()` is called, **no file is written for `architecture`**. Only `sabdx-architecture/SKILL.md` ends up on disk. The `replaces` field is a resolver-level concern; it does not need to be written to SKILL.md frontmatter.
+
+### KD-4: `replaces` field is stripped before writing SKILL.md
+`writeInlineSkills()` uses the skill's `name`, `description`, and `body` for the SKILL.md frontmatter. The `replaces` field is simply ignored during file writing — no changes needed in `util.ts`.
+
+### KD-5: `replaces` field is NOT persisted in `config.lock.yaml`
+The lock file records `logical_config`, which is the *post-dedup* skills list. Replaced skills never appear in the lock file.
+
+### KD-6: Ordering — extensions should register skills after process
+The resolver processes facets in `sortFacets()` order. The `architecture` facet comes after `process`, so extension skills are appended after the generic ones. The last-writer-wins Map dedup naturally lets extension skills win. But `replaces` is independent of ordering — it is an explicit declaration.
+
+## Notes
+
+### Full flow for the sadb-frontend scenario
+1. `codemcp-workflows-skilled` recipe runs → appends to `result.skills`: `[starting-project, architecture, application-design, coding, testing]`
+2. `sabdx-frontend` recipe runs → appends: `[sabdx-tasks, sabdx-starting-project{replaces:["starting-project"]}, sabdx-architecture{replaces:["architecture"]}, sabdx-application-design{replaces:["application-design"]}, sabdx-coding{replaces:["coding"]}, sabdx-testing{replaces:["testing"]}, tdd]`
+3. `conventional-commits` recipe runs → appends: `[conventional-commits]`
+4. Raw merged list: 13 skills
+5. Post-dedup (name Map + replaces filter): 8 skills remain — `[sabdx-tasks, sabdx-starting-project, sabdx-architecture, sabdx-application-design, sabdx-coding, sabdx-testing, tdd, conventional-commits]`
+6. `writeInlineSkills()` writes SKILL.md files for the 6 inline sabdx-* skills under `.ade/skills/<name>/`
+7. `installSkills()` installs all 8 into `.agentskills/skills/`
+
+### What files exist on disk after setup
+- `.ade/skills/sabdx-tasks/SKILL.md`
+- `.ade/skills/sabdx-starting-project/SKILL.md`
+- `.ade/skills/sabdx-architecture/SKILL.md`
+- `.ade/skills/sabdx-application-design/SKILL.md`
+- `.ade/skills/sabdx-coding/SKILL.md`
+- `.ade/skills/sabdx-testing/SKILL.md`
+- NO `.ade/skills/architecture/SKILL.md` (replaced, never written)
+- NO `.ade/skills/starting-project/SKILL.md` (replaced, never written)
+- etc.
+
+### The `tdd` skill from the extension — no `replaces` needed
+`tdd` is an external skill (`source: "mrsimpson/skills-coding"`) and there is no generic `tdd` skill in `codemcp-workflows-skilled`. No clash.
+
+---
+*This plan is maintained by the LLM and uses beads CLI for task management. Tool responses provide guidance on which bd commands to use for task management.*