`install -i codex` (6.3.0) leaves stale skill wrappers pointing at deleted files

[three-rings-enterprises]

Version: bmad-method@6.3.0 (latest)
Command: bmad-method install -f -i codex (via npm run bmad:refresh)

Bug: After install completes, .agents/skills/ contains two parallel sets
of BMAD skills:

1. New, self-contained skills — .agents/skills/bmad-* (no -bmm-
   middle segment). These have persona/menu inline and work correctly.
2. Stale wrapper skills — .agents/skills/bmad-bmm-* and
   .agents/skills/bmad-agent-bmm-* (~32 total). Their SKILL.md files
   still start with:

or

But the same install deletes _bmad/core/tasks/workflow.xml,
_bmad/bmm/agents/*.md, and _bmad/bmm/workflows/** as part of the
move to skills-based architecture. Invoking any of these wrappers in
Codex fails immediately at activation with missing-file errors.

Expected: Install either removes the legacy bmad-bmm-* /
bmad-agent-bmm-* wrappers atomically, or rewrites them to match the
new self-contained skill pattern used by the bmad-* siblings.

Reproduction:

1. Fresh repo, run bmad-method install -i codex on bmad-method@6.3.0.
2. ls .agents/skills/ | grep -E "^bmad-(bmm-|agent-bmm-)" — 32 entries.
3. grep -l "_bmad/core/tasks/workflow.xml\|_bmad/bmm/agents/" .agents/skills/bmad-bmm-*/SKILL.md .agents/skills/bmad-agent-bmm-*/SKILL.md — all match.
4. test -f _bmad/core/tasks/workflow.xml && echo exists || echo missing — missing.

Workaround: rm -rf .agents/skills/bmad-bmm-* .agents/skills/bmad-agent-bmm-* — the surviving self-contained skills provide equivalent coverage.

Impact: Reported externally by automated PR review (OpenAI Codex) as P1 in downstream projects consuming the Codex tool target.

[coderabbitai]

🔗 Related PRs

#1729 - feat: migrate Codex installer from .codex/prompts to .agents/skills format [merged]
#1868 - refactor(skills): add SKILL.md entrypoint to skill directories [merged]
#1936 - refactor(skills): convert create-architecture workflow to native skill [merged]
#1941 - Convert code-review workflow to native skill packaging [merged]
#2078 - refactor(installer): remove legacy workflow, task, and agent IDE generators [merged]

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