Bug: ~~placeholder strings shown verbatim to users in bio-research, enterprise-search, and sales commands

[marlonbarreto-git]

Problem

Several plugin command and skill files contain ~~category placeholder strings that are displayed verbatim to users instead of being resolved to actual tool names. This affects the user experience by showing meaningless placeholders like ~~literature database instead of "PubMed" or "bioRxiv".

Affected Files

bio-research/commands/start.md — 12+ instances

The welcome message shown when a user runs the bio-research start command contains:

- ~~literature database — biomedical literature search
- ~~literature database — preprint access (biology and medicine)
- ~~journal access — academic publications
- ~~chemical database — compound and bioactivity data
...
1. "Search ~~literature database for recent papers on [topic]"
3. "Search ~~chemical database for compounds targeting [protein]"

The actual MCP servers configured in bio-research/.mcp.json are pubmed, biorxiv, wiley, chembl, etc. — but the start command never maps these to the ~~ placeholders. Users see literal ~~literature database in their welcome text.

enterprise-search/commands/search.md — User-visible error message

When no connectors are configured, users see:

Check your MCP settings to add ~~chat, ~~email, ~~cloud storage, or other tools.
Supported sources: ~~chat, ~~email, ~~cloud storage, ~~project tracker, ~~CRM, ~~knowledge base

Instead of helpful text like "Slack, Gmail, Google Drive, Jira, Salesforce, Confluence".

sales/skills/draft-outreach/SKILL.md — Lines 103 and 439

Draft created - check ~~email

Users completing a draft see check ~~email instead of "check Gmail" or "check Outlook".

Root Cause

The ~~category convention (documented in each plugin's CONNECTORS.md) is designed so that skills reference tool categories rather than specific products. However, there appears to be no runtime resolution mechanism that maps ~~category to the user's actual connected tool name. The placeholders pass through to the user interface as-is.

Expected Behavior

One of:

1. Runtime resolution: ~~literature database resolves to "PubMed" (or whatever the user has connected) before being shown
2. Static fallback: Command files use the specific tool names from .mcp.json as defaults (e.g., "PubMed/bioRxiv" instead of ~~literature database)
3. Generic but readable: Replace ~~category with human-readable generic terms (e.g., "your literature search tool" instead of ~~literature database)

Impact

• New users see cryptic ~~ prefixed strings in their first interaction with these plugins
• The bio-research plugin is particularly affected — 12+ placeholder instances in the welcome message make the entire onboarding experience feel broken
• Enterprise-search error messages are unhelpful when they reference placeholder categories instead of actual tool names

Happy to submit a PR with Option 2 (static fallback names from .mcp.json) if the team prefers that approach.