addressed coverage and docs issues

[jonathanMLDev]

Pull Request

Coverage & changelog

• vitest.config.ts — Global coverage.thresholds (lines 73, statements 72, branches 58, functions 76) from the last measured run, with a short rationale comment.
• CHANGELOG.md — [Unreleased] updated: explicit threshold percents, docs/examples/link-check bullets, CI quality job description.

Docs (docs/)

• docs/README.md — Index of all guides.
• docs/TOOLS.md — All 9 tools: parameters, success shapes, suggest-flow, namespace consistency, rerank/reranked behavior and pointer to migration/README errors.
• docs/CONFIGURATION.md — ServerConfig, env vars, CLI flags, precedence.
• docs/SECURITY.md — Keys, logger redaction patterns, Dockerfile non-root user, reporting.
• docs/CONTRIBUTING.md — Setup and npm scripts.
• docs/CI_CD.md — ci.yml matrix, CodeQL, SBOM, Codecov, publish workflow.
• docs/FAQ.md — Common questions.
• docs/MIGRATION.md — v0.2.0-style section: four breaking themes + namespace trimming.
• docs/RELEASING.md — Release → npm flow.

Examples

• examples/suggest-flow-demo.ts, examples/guided-query-demo.ts, examples/library-embedding-demo.ts — Same @will-cppa/pinecone-read-only-mcp import style as the existing demo; gated paths print doc-only mode without PINECONE_API_KEY.
• examples/README.md — Table updated for all four demos.

README

• Doc table: docs/RELEASING.md, docs/CONTRIBUTING.md, docs/SECURITY.md (fixes previously broken root-only links).
• Library embedding subsection — single-process setupServer guidance (no teardownServer in code yet; recommends separate processes until a lifecycle API ships).
• Examples table + run line.
• Success payloads note → docs/TOOLS.md for rerank / degraded envelope status.

CI & link check

• .github/workflows/ci.yml — quality job runs markdown-link-check on README.md, CHANGELOG.md, and every docs/**/*.md.
• .markdown-link-check.json — Skips http(s):// and mailto: so CI validates relative links only (avoids flaky external/mailto checks).

Related Issues

close #90
close #92
close #93
close #95

Summary by CodeRabbit

Release Notes

• Documentation

  • Added comprehensive guides for configuration, security, tools reference, migration, contribution, CI/CD, and FAQ.
  • Expanded README with library embedding details and examples table.
  • New migration guide for version 0.2.0 updates.

• New Features

  • Three new example scripts demonstrating suggest-flow, guided-query, and library-embedding patterns.

• Tests

  • Added coverage threshold enforcement to reduce flakiness.

• Chores

  • Enhanced CI with markdown link validation.
  • Updated benchmark baseline data.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 29a72b16-c54e-482e-a4e9-3724e8458383

📥 Commits

Reviewing files that changed from the base of the PR and between 327b5ad and 7cd8945.

📒 Files selected for processing (9)

• .github/workflows/ci.yml
• CHANGELOG.md
• README.md
• docs/CI_CD.md
• docs/CONTRIBUTING.md
• docs/SECURITY.md
• examples/library-embedding-demo.ts
• package.json
• scripts/docs-link-check.mjs

📝 Walkthrough

Walkthrough

This PR fulfills four linked issues by delivering a comprehensive documentation ecosystem: eight new guide documents (TOOLS, CONFIGURATION, SECURITY, CONTRIBUTING, CI_CD, FAQ, MIGRATION, docs/README), three worked examples (suggest-flow, guided-query, library-embedding), CI markdown-link validation, vitest coverage thresholds, and updated benchmarks to address missing documentation, migration guidance, examples, and coverage enforcement.

Changes

Documentation Ecosystem and Examples Suite

Layer / File(s)	Summary
Documentation navigation and root README updates README.md, docs/README.md, .github/workflows/ci.yml, .markdown-link-check.json, CHANGELOG.md	Root README now links to docs/ guides and clarifies library embedding and rerank behavior. docs/README.md serves as an index to TOOLS, CONFIGURATION, SECURITY, CONTRIBUTING, CI_CD, FAQ, MIGRATION, and RELEASING guides. CI adds a markdown-link-check step validating all internal documentation links using a centralized configuration file. CHANGELOG documents the expanded CI matrix, quality checks, vitest coverage thresholds, and @vitest/coverage-v8 addition.
Core reference documentation docs/TOOLS.md, docs/CONFIGURATION.md, docs/SECURITY.md, docs/CONTRIBUTING.md	TOOLS.md documents 9 MCP tools with suggest-flow gate rules, request/response shapes, tool ordering constraints, and a cheat sheet for manual vs. single-shot flows. CONFIGURATION.md specifies precedence order (CLI > env > defaults), all ServerConfig fields with environment mappings, CLI flag mappings, and library embedding sequence. SECURITY.md covers API key handling, log redaction, Docker hardening, supply-chain controls (npm audit, SBOM), and vulnerability reporting. CONTRIBUTING.md details Node/npm setup, npm scripts, TypeScript strictness conventions, and documentation maintenance.
Specialized guides docs/CI_CD.md, docs/FAQ.md, docs/MIGRATION.md, docs/RELEASING.md	CI_CD.md documents the CI matrix job (OSes, Node versions, SBOM, Codecov), quality job (npm audit, markdown-link-check), CodeQL scanning, and GitHub Release publish workflow. FAQ.md clarifies suggest-flow gating for query, documents query preset unification, and explains testing bypass via environment variable. MIGRATION.md provides v0.2.0 upgrade guide: namespace trimming, ToolError shape replacement, status: 'error' field removal, recommended_tool value changes, and query_fast/query_detailed → query consolidation. RELEASING.md describes GitHub Release-triggered publish workflow, NPM_TOKEN secret, and SERVER_VERSION sourcing.
Worked examples demonstrating key workflows examples/README.md, examples/suggest-flow-demo.ts, examples/guided-query-demo.ts, examples/library-embedding-demo.ts	examples/README.md links to three new example scripts. suggest-flow-demo.ts demonstrates the multi-step suggest-then-query workflow with namespace trimming and preset alignment. guided-query-demo.ts demonstrates single-call guided_query orchestration with decision trace output and config resolution. library-embedding-demo.ts demonstrates programmatic setupServer usage with setPineconeClient initialization. All include error handling and conditional execution based on PINECONE_API_KEY.
Test infrastructure: vitest coverage thresholds and benchmarks vitest.config.ts, benchmarks/baseline.json	vitest.config.ts adds documented global coverage gates (lines, statements, branches, functions) with explicit threshold values to enforce regression detection. benchmarks/baseline.json establishes baseline measurements: generated timestamp, Node.js version, warmup/measured iteration counts, and percentile timings (p50, p95, p99) for all named benchmark scenarios.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

Suggested labels

enhancement

Suggested reviewers

• wpak-ai
• AuraMindNest

Poem

📚 The docs arrived like spring blooms,
Nine tools mapped in spacious rooms,
From config tips to examples run,
The repository's knowledge is now one.
Link-checked and covered—let the tests have fun! 🐰

🚥 Pre-merge checks | ✅ 3 | ❌ 2

❌ Failed checks (1 warning, 1 inconclusive)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.
Title check	❓ Inconclusive	Title is vague and generic, using non-descriptive terms like "addressed issues" without conveying the primary scope or nature of changes.	Use a more specific title that highlights the main contribution, e.g., 'Add comprehensive documentation, examples, and coverage thresholds' or 'Document tools, config, security, and add worked examples'.

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Linked Issues check	✅ Passed	All four linked issues (#90, #92, #93, #95) are comprehensively addressed: docs/ directory created with 8+ files, MIGRATION.md with breaking changes, three worked examples added, and vitest coverage thresholds configured.
Out of Scope Changes check	✅ Passed	All changes are within scope of the four linked issues. Updates to .github/workflows/ci.yml and .markdown-link-check.json support the docs link-check requirement (#90). Updates to README.md and examples/ directly fulfill acceptance criteria. No unrelated changes detected.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
⚠️ Please upload report for BASE (main@66fe34a). Learn more about missing BASE report.

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #98   +/-   ##
=======================================
  Coverage        ?   80.04%           
=======================================
  Files           ?       34           
  Lines           ?     1258           
  Branches        ?      421           
=======================================
  Hits            ?     1007           
  Misses          ?      249           
  Partials        ?        2           

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[coderabbitai]

Actionable comments posted: 2

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@docs/CONTRIBUTING.md`:
- Line 11: Replace the incorrect repository URL string "git clone
https://github.com/CppDigest/pinecone-read-only-mcp-typescript.git" in
CONTRIBUTING.md with the correct upstream clone command "git clone
https://github.com/cppalliance/pinecone-read-only-mcp-typescript.git" so new
contributors clone the intended repo; update any surrounding text if it repeats
the wrong hostname.

In `@examples/library-embedding-demo.ts`:
- Around line 25-27: The code currently supplies a dummy API key via the apiKey
const and then calls resolveConfig; instead require PINECONE_API_KEY explicitly:
remove the 'demo-key-for-types' fallback, read and trim
process.env['PINECONE_API_KEY'], and if it's missing or empty log/print a clear
doc-only message and exit early (before calling resolveConfig) so resolveConfig
isn't invoked with a fake key; update references to the apiKey variable and the
resolveConfig call in examples/library-embedding-demo.ts accordingly.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: c7259842-75ea-447c-97d8-4f5d976534bc

📥 Commits

Reviewing files that changed from the base of the PR and between 4eadc6c and 327b5ad.

📒 Files selected for processing (19)

• .github/workflows/ci.yml
• .markdown-link-check.json
• CHANGELOG.md
• README.md
• benchmarks/baseline.json
• docs/CI_CD.md
• docs/CONFIGURATION.md
• docs/CONTRIBUTING.md
• docs/FAQ.md
• docs/MIGRATION.md
• docs/README.md
• docs/RELEASING.md
• docs/SECURITY.md
• docs/TOOLS.md
• examples/README.md
• examples/guided-query-demo.ts
• examples/library-embedding-demo.ts
• examples/suggest-flow-demo.ts
• vitest.config.ts