docs(pubmed): add config command documentation to PR description

Author: WorkBuddy

PULL_REQUEST.md

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+# Pull Request: Add PubMed Adapter
+
+## Summary
+
+This PR adds comprehensive PubMed academic literature search capabilities to OpenCLI, enabling researchers and clinicians to access the PubMed database directly from the command line.
+
+## Features
+
+### New Commands (6 total)
+
+| Command | Description |
+|---------|-------------|
+| `pubmed search` | Advanced article search with multiple filters |
+| `pubmed article` | Detailed article metadata retrieval |
+| `pubmed author` | Search by author name and affiliation |
+| `pubmed citations` | Get citation relationships |
+| `pubmed related` | Find semantically similar articles |
+| `pubmed config` | Configure API key for higher rate limits |
+
+### Key Capabilities
+
+- **Advanced Search Filters**: date range, author, journal, article type, abstract availability, free full text, human studies, language
+- **Complete Author Information**: first author, corresponding author, all authors, affiliations
+- **Publication Metadata**: title, abstract, journal, volume, issue, pages, publication date
+- **Academic Identifiers**: PMID, DOI, PMC ID
+- **Classification**: MeSH terms, keywords, article type
+- **Citation Analysis**: find articles that cite a given article or articles cited by it
+- **Related Articles**: discover semantically similar articles using PubMed's algorithm
+
+## API Integration
+
+Uses NCBI E-utilities APIs:
+- **ESearch**: Search for articles and retrieve PMIDs
+- **ESummary**: Get summary information for PMIDs
+- **EFetch**: Retrieve full article details including abstracts
+- **ELink**: Get citation relationships and related articles
+
+## Technical Implementation
+
+- **Language**: TypeScript with full type safety
+- **Strategy**: `Strategy.PUBLIC` (PubMed E-utilities is a public API)
+- **Rate Limiting**: Automatic delays to respect NCBI limits (3 req/s public, 10 req/s with API key)
+- **Error Handling**: Consistent use of `CliError` for all error cases
+- **Code Quality**: Follows existing OpenCLI patterns (similar to arXiv adapter)
+
+## Files Added
+
+```
+clis/pubmed/
+├── utils.ts      # Shared utilities for API calls and data parsing
+├── search.ts     # Article search with advanced filters
+├── article.ts    # Detailed article information
+├── author.ts     # Author-based search
+├── citations.ts  # Citation relationships
+├── related.ts    # Related articles discovery
+└── config.ts     # API key configuration for higher rate limits
+```
+
+## Usage Examples
+
+```bash
+# Search with filters
+opencli pubmed search "machine learning cancer" --year-from 2023 --has-abstract
+
+# Get article details
+opencli pubmed article 37780221 --format json
+
+# Search by author
+opencli pubmed author "Smith J" --affiliation "Stanford" --position first
+
+# Citation analysis
+opencli pubmed citations 37780221 --direction citedby --limit 50
+
+# Find related articles
+opencli pubmed related 37780221 --score
+
+# Configure API key for higher rate limits (10 req/s vs 3 req/s)
+opencli pubmed config set --key api-key --value YOUR_NCBI_API_KEY
+
+# View current configuration
+opencli pubmed config get
+
+# Remove API key
+opencli pubmed config remove --key api-key
+```
+
+## Testing
+
+- [x] Built successfully with `npm run build`
+- [x] Manifest compiled: 260 entries (121 YAML, 139 TS)
+- [x] All TypeScript files compile without errors
+- [ ] Runtime testing (requires NCBI API access)
+
+## Documentation
+
+A comprehensive README is available in the contribution package with:
+- Installation instructions
+- Detailed usage examples
+- API reference
+- Rate limit information
+- File structure explanation
+
+## Rate Limits & API Key Configuration
+
+The adapter implements automatic rate limiting:
+- **Without API key**: 350ms delay between requests (≈3 req/s)
+- **With API key**: 100ms delay between requests (≈10 req/s)
+
+### Getting an API Key
+
+1. Create an NCBI account at https://www.ncbi.nlm.nih.gov/account/
+2. Go to https://www.ncbi.nlm.nih.gov/account/settings/
+3. Generate an API key
+
+### Configuring Your API Key
+
+```bash
+# Set your API key
+opencli pubmed config set --key api-key --value YOUR_API_KEY
+
+# Set your email (recommended for identification)
+opencli pubmed config set --key email --value your@email.com
+
+# View current configuration
+opencli pubmed config get
+
+# Remove configuration
+opencli pubmed config remove --key api-key
+```
+
+Configuration is stored in `~/.opencli/pubmed-config.json`.
+
+### Environment Variables
+
+Alternatively, you can use environment variables:
+- `NCBI_API_KEY` - Your NCBI API key
+- `NCBI_EMAIL` - Your email address
+
+## Backwards Compatibility
+
+This is a new adapter with no impact on existing functionality.
+
+## Checklist
+
+- [x] Code follows OpenCLI conventions
+- [x] TypeScript types are properly defined
+- [x] Error handling uses CliError
+- [x] Rate limiting is implemented
+- [x] Build passes successfully
+- [x] No breaking changes to existing code
+
+## Author
+
+**WorkBuddy** - An AI assistant helping researchers access scientific literature more efficiently.
+
+## References
+
+- [NCBI E-utilities Documentation](https://www.ncbi.nlm.nih.gov/books/NBK25501/)
+- [PubMed](https://pubmed.ncbi.nlm.nih.gov/)
+
+---
+
+**Related Issue**: N/A (new feature)
+
+**Breaking Changes**: None
+
+**Dependencies**: None (uses native fetch API)