Templates still reference deprecated/ghost tools (consult_expert, research, get_canonical_persona, project_profile)

[wtthornton]

Problem

v2.3.0 removed tapps_project_profile, tapps_manage_experts, tapps_get_canonical_persona, and tapps_list_experts from the MCP server. tapps_consult_expert and tapps_research return TOOL_DEPRECATED errors. However, the upgrade templates still generate files that reference these tools as primary paths.

Affected Templates

After running tapps_upgrade with v2.3.0, the following generated files still reference deprecated/ghost tools:

File	Ghost/Deprecated Reference
CLAUDE.md template	tapps_project_profile(), tapps_get_canonical_persona(), tapps_consult_expert() as primary
AGENTS.md template	tapps_consult_expert domain hints section, tapps_project_profile in workflow
.claude/agents/tapps-researcher.md	tapps_research, tapps_consult_expert, tapps_get_canonical_persona
.claude/agents/tapps-review-fixer.md	tapps_get_canonical_persona
.claude/agents/tapps-reviewer.md	tapps_get_canonical_persona
.claude/agents/tapps-validator.md	tapps_get_canonical_persona
.claude/skills/tapps-research/SKILL.md	tapps_research, tapps_consult_expert in allowed-tools
.claude/skills/tapps-security/SKILL.md	tapps_consult_expert in allowed-tools
.claude/skills/tapps-tool-reference/SKILL.md	tapps_project_profile, tapps_consult_expert, tapps_research, tapps_list_experts
.claude/rules/python-quality.md	tapps_research
.github/copilot-instructions.md	tapps_project_profile, tapps_consult_expert
.github/agents/tapps-researcher.md	tapps_research, tapps_consult_expert in tool list

Expected Behavior

Templates should not reference tools that:

1. Are not registered in the MCP server (ghost tools)
2. Return TOOL_DEPRECATED errors

For deprecated tools with stubs (tapps_consult_expert, tapps_research), templates should use preferred/fallback framing pointing to the replacement path.

Suggested Fix

Update all Jinja/string templates in packages/tapps-mcp/src/tapps_mcp/templates/ to:

• Remove tapps_project_profile, tapps_get_canonical_persona, tapps_manage_experts, tapps_list_experts
• Mark tapps_consult_expert and tapps_research as [DEPRECATED] with alternatives noted
• Use tapps_lookup_docs as the primary research tool