diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index a74c59e..e1f96e3 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,6 +1,6 @@
 name: CI
 permissions:
-  contents: read
+  contents: write
 
 on:
   push:
@@ -35,7 +35,7 @@ jobs:
         # For dev branch: exclude optional tests (docker, llm, performance, pydantic_ai)
         if [ "${{ github.ref }}" = "refs/heads/main" ]; then
           echo "Running all tests including optional tests for main branch"
-          pytest tests/ --cov=DeepResearch --cov-report=xml --cov-report=term-missing --junitxml=junit.xml -o junit_family=legacy
+          pytest tests/ -m "not containerized" --cov=DeepResearch --cov-report=xml --cov-report=term-missing --junitxml=junit.xml -o junit_family=legacy
         else
           echo "Running tests excluding optional tests for dev branch"
           pytest tests/ -m "not optional and not containerized" --cov=DeepResearch --cov-report=xml --cov-report=term-missing --junitxml=junit.xml -o junit_family=legacy
@@ -43,35 +43,115 @@ jobs:
 
     - name: Run bioinformatics unit tests (all branches)
       run: |
-        echo "🧬 Running bioinformatics unit tests..."
+        echo "Running bioinformatics unit tests..."
         pytest tests/test_bioinformatics_tools/ -m "not containerized" --cov=DeepResearch --cov-append --cov-report=xml --cov-report=term-missing --junitxml=junit-bioinformatics.xml -o junit_family=legacy
 
     - name: Run bioinformatics containerized tests (main branch only)
       if: github.ref == 'refs/heads/docker'
       run: |
-        echo "🐳 Running bioinformatics containerized tests..."
+        echo "Running bioinformatics containerized tests..."
         # Check if Docker is available and bioinformatics images exist
         if docker --version >/dev/null 2>&1; then
-          make test-bioinformatics-containerized || echo "⚠️  Containerized tests failed, but continuing..."
+          make test-bioinformatics-containerized || echo "Containerized tests failed, but continuing..."
         else
-          echo "⚠️  Docker not available, skipping containerized tests"
+          echo "Docker not available, skipping containerized tests"
         fi
 
+    - name: Debug coverage files
+      run: |
+        echo "Checking for coverage files..."
+        ls -la coverage.xml junit.xml junit-bioinformatics.xml || echo "Some files missing"
+        head -20 coverage.xml || echo "Coverage file not readable"
+
+    # Codecov upload steps - These steps will NOT fail the CI even if uploads fail
+    # Tests will pass regardless of Codecov upload status
+    - name: Configure Codecov repository setup
+      run: |
+        # Check if CODECOV_TOKEN is available and set HAS_CODECOV_TOKEN flag
+        if [ -n "${CODECOV_TOKEN}" ]; then
+          echo "📊 Codecov token found - uploads will be enabled"
+          echo "🔗 Repository: ${{ github.repository }}"
+          echo "📈 Coverage reports will be uploaded to Codecov"
+          echo "✅ Codecov uploads enabled for this run"
+          echo "HAS_CODECOV_TOKEN=true" >> $GITHUB_ENV
+        else
+          echo "⚠️ CODECOV_TOKEN not found - uploads will be skipped"
+          echo "💡 To enable Codecov uploads:"
+          echo "   1. Go to https://codecov.io/gh/${{ github.repository }}/settings"
+          echo "   2. Generate a repository upload token"
+          echo "   3. Add it as CODECOV_TOKEN secret in repository settings"
+          echo "   4. Repository will be auto-detected on first upload"
+          echo "HAS_CODECOV_TOKEN=false" >> $GITHUB_ENV
+        fi
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+    - name: Display coverage summary
+      run: |
+        echo "📈 Local Coverage Summary:"
+        echo "=========================="
+        if command -v coverage >/dev/null 2>&1; then
+          python -m coverage report --include="DeepResearch/*" --omit="*/tests/*,*/test_*" || echo "Coverage report generation failed"
+        else
+          echo "Coverage.py not available for summary"
+        fi
+        echo ""
+        echo "📁 Coverage files generated:"
+        ls -lh *.xml 2>/dev/null || echo "No XML coverage files found"
+        echo ""
+        echo "💡 To view detailed coverage: python -m coverage html && open htmlcov/index.html"
+
     - name: Upload coverage to Codecov
+      if: env.HAS_CODECOV_TOKEN == 'true'
       uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        slug: Josephrp/DeepCritical
         files: ./coverage.xml
-        fail_ci_if_error: true
+        fail_ci_if_error: false
         verbose: true
+        slug: ${{ github.repository }}
+        name: "${{ github.ref_name }} - Python ${{ matrix.python-version || '3.11' }}"
+      continue-on-error: true
 
     - name: Upload test results to Codecov
-      if: ${{ !cancelled() }}
+      if: env.HAS_CODECOV_TOKEN == 'true' && !cancelled()
       uses: codecov/test-results-action@v1
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        slug: Josephrp/DeepCritical
+        files: ./junit.xml
+        verbose: true
+        slug: ${{ github.repository }}
+      continue-on-error: true
+
+    - name: Upload bioinformatics test results to Codecov
+      if: env.HAS_CODECOV_TOKEN == 'true' && !cancelled()
+      uses: codecov/test-results-action@v1
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        files: ./junit-bioinformatics.xml
+        verbose: true
+        slug: ${{ github.repository }}
+      continue-on-error: true
+
+    - name: Codecov upload summary
+      if: env.HAS_CODECOV_TOKEN == 'false'
+      run: |
+        echo "ℹ️ Codecov uploads were skipped because CODECOV_TOKEN is not configured"
+        echo ""
+        echo "📋 Setup Instructions:"
+        echo "======================"
+        echo "1. Visit: https://codecov.io/gh/${{ github.repository }}"
+        echo "2. Sign in with GitHub"
+        echo "3. Repository should auto-appear"
+        echo "4. Go to Settings → Repository Upload Token"
+        echo "5. Generate and copy the token"
+        echo "6. Go to GitHub repo Settings → Secrets and variables → Actions"
+        echo "7. Add new repository secret: CODECOV_TOKEN"
+        echo "8. Paste the token value"
+        echo "9. Codecov uploads will work on next run"
+        echo ""
+        echo "✅ CI will pass regardless of Codecov upload status"
+        echo "📊 Coverage reports were still generated locally for inspection"
 
     - name: Run VLLM tests (optional, manual trigger only)
       if: github.event_name == 'workflow_dispatch' || contains(github.event.head_commit.message, '[vllm-tests]')
diff --git a/.github/workflows/test-enhanced.yml b/.github/workflows/test-enhanced.yml
index c540fe2..ba1d08e 100644
--- a/.github/workflows/test-enhanced.yml
+++ b/.github/workflows/test-enhanced.yml
@@ -55,11 +55,13 @@ jobs:
         run: make test-performance
 
       - name: Upload coverage reports
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v5
         if: matrix.python-version == '3.11'
         with:
+          token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
           fail_ci_if_error: false
+          slug: ${{ github.repository }}
 
       - name: Upload test artifacts
         uses: actions/upload-artifact@v4
diff --git a/.github/workflows/test-optional.yml b/.github/workflows/test-optional.yml
index 4bb9598..fb9910a 100644
--- a/.github/workflows/test-optional.yml
+++ b/.github/workflows/test-optional.yml
@@ -98,9 +98,10 @@ jobs:
 
     - name: Upload coverage to Codecov (optional tests)
       if: always()
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         files: ./coverage.xml
         fail_ci_if_error: false
         verbose: true
+        slug: ${{ github.repository }}
diff --git a/README.md b/README.md
index 8e3e889..912beeb 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 # 🚀 DeepCritical: Building a Highly Configurable Deep Research Agent Ecosystem
 
-[![Documentation](https://img.shields.io/badge/docs-latest-blue.svg)][![(https://deepcritical.github.io/DeepCritical)]
-https://codecov.io/gh/DeepCritical/DeepCritical/branch/dev/graph/badge.svg?token=N8H1DOUXQL]
+[![Documentation](https://img.shields.io/badge/docs-latest-blue.svg)](https://deepcritical.github.io/DeepCritical)
+[![codecov](https://codecov.io/gh/DeepCritical/DeepCritical/branch/dev/graph/badge.svg)](https://codecov.io/gh/DeepCritical/DeepCritical)
 
 ## Vision: From Single Questions to Research Field Generation
 
@@ -618,6 +618,34 @@ Prompt templates in `configs/prompts/`:
 
 ## 🔧 Development
 
+### Development
+
+### Codecov Setup
+
+To enable coverage reporting with Codecov:
+
+1. **Set up the repository in Codecov:**
+   - Visit [https://app.codecov.io/gh/DeepCritical/DeepCritical](https://app.codecov.io/gh/DeepCritical/DeepCritical)
+   - Click "Add new repository" or "Setup repo" if prompted
+   - Follow the setup wizard to connect your GitHub repository
+
+2. **Generate a Codecov token:**
+   - In Codecov, go to your repository settings
+   - Navigate to "Repository Settings" > "Tokens"
+   - Generate a new token with "upload" permissions
+
+3. **Add the token as a GitHub secret:**
+   - In your GitHub repository, go to Settings > Secrets and variables > Actions
+   - Click "New repository secret"
+   - Name: `CODECOV_TOKEN`
+   - Value: Your Codecov token from step 2
+
+4. **Verify setup:**
+   - Push a commit to trigger the CI pipeline
+   - Check that coverage reports appear in Codecov
+
+The CI workflow will automatically upload coverage reports once the repository is configured in Codecov and the token is added as a secret.
+
 ### Development with uv
 
 ```bash
diff --git a/codecov.yml b/codecov.yml
index ffe4096..6fe8abf 100644
--- a/codecov.yml
+++ b/codecov.yml
@@ -10,9 +10,167 @@ coverage:
         threshold: 1%
 
 comment:
-  layout: "reach,diff,flags,tree"
+  layout: "condensed_header, condensed_files, condensed_footer"
   behavior: default
   require_changes: false
+  hide_project_coverage: true
+
+component_management:
+  default_rules:
+    statuses:
+      - type: project
+        target: auto
+        threshold: 1%
+        branches:
+          - "!main"
+  individual_components:
+    # Core Architecture Components
+    - component_id: core_app
+      name: Core Application
+      paths:
+        - DeepResearch/app.py
+        - DeepResearch/__init__.py
+
+    - component_id: agents
+      name: Agents
+      paths:
+        - DeepResearch/agents.py
+        - DeepResearch/src/agents/**
+
+    - component_id: datatypes
+      name: Data Types
+      paths:
+        - DeepResearch/src/datatypes/**
+
+    - component_id: tools
+      name: Tools
+      paths:
+        - DeepResearch/tools/**
+        - DeepResearch/src/tools/**
+
+    - component_id: statemachines
+      name: State Machines
+      paths:
+        - DeepResearch/src/statemachines/**
+        - configs/statemachines/**
+
+    - component_id: utils
+      name: Utilities
+      paths:
+        - DeepResearch/src/utils/**
+
+    - component_id: models
+      name: Models
+      paths:
+        - DeepResearch/src/models/**
+
+    - component_id: prompts
+      name: Prompts
+      paths:
+        - DeepResearch/src/prompts/**
+        - configs/prompts/**
+
+    - component_id: workflow_patterns
+      name: Workflow Patterns
+      paths:
+        - DeepResearch/src/workflow_patterns.py
+        - DeepResearch/examples/workflow_patterns_demo.py
+
+    # Specialized Components
+    - component_id: bioinformatics
+      name: Bioinformatics
+      paths:
+        - DeepResearch/src/tools/bioinformatics/**
+        - DeepResearch/src/agents/bioinformatics_agents.py
+        - DeepResearch/src/datatypes/bioinformatics*.py
+        - DeepResearch/src/prompts/bioinformatics*.py
+        - DeepResearch/src/statemachines/bioinformatics_workflow.py
+        - configs/bioinformatics/**
+        - tests/test_bioinformatics_tools/**
+        - docker/bioinformatics/**
+
+    - component_id: deep_agent
+      name: Deep Agent
+      paths:
+        - DeepResearch/src/agents/deep_agent*.py
+        - DeepResearch/src/datatypes/deep_agent*.py
+        - DeepResearch/src/prompts/deep_agent*.py
+        - DeepResearch/src/statemachines/deep_agent*.py
+        - DeepResearch/src/tools/deep_agent*.py
+        - configs/deep_agent/**
+
+    - component_id: rag
+      name: RAG
+      paths:
+        - DeepResearch/src/agents/rag_agent.py
+        - DeepResearch/src/datatypes/rag.py
+        - DeepResearch/src/prompts/rag.py
+        - DeepResearch/src/statemachines/rag_workflow.py
+        - configs/rag/**
+
+    - component_id: vllm
+      name: VLLM Integration
+      paths:
+        - DeepResearch/src/agents/vllm_agent.py
+        - DeepResearch/src/datatypes/vllm*.py
+        - DeepResearch/src/prompts/vllm_agent.py
+        - configs/vllm/**
+        - tests/test_llm_framework/**
+        - tests/test_prompts_vllm/**
+        - test_artifacts/vllm_tests/**
+
+    - component_id: deepsearch
+      name: Deep Search
+      paths:
+        - DeepResearch/src/tools/deepsearch*.py
+        - DeepResearch/src/statemachines/deepsearch_workflow.py
+        - configs/deepsearch/**
+
+    # Test Components
+    - component_id: test_bioinformatics
+      name: Bioinformatics Tests
+      paths:
+        - tests/test_bioinformatics_tools/**
+
+    - component_id: test_vllm
+      name: VLLM Tests
+      paths:
+        - tests/test_llm_framework/**
+        - tests/test_prompts_vllm/**
+
+    - component_id: test_pydantic_ai
+      name: Pydantic AI Tests
+      paths:
+        - tests/test_pydantic_ai/**
+
+    - component_id: test_docker_sandbox
+      name: Docker Sandbox Tests
+      paths:
+        - tests/test_docker_sandbox/**
+
+    - component_id: test_core
+      name: Core Tests
+      paths:
+        - tests/test_*.py
+
+    # Configuration and Documentation
+    - component_id: configuration
+      name: Configuration
+      paths:
+        - configs/**
+        - pyproject.toml
+        - codecov.yml
+
+    - component_id: scripts
+      name: Scripts
+      paths:
+        - DeepResearch/scripts/**
+        - scripts/**
+
+    - component_id: docker
+      name: Docker
+      paths:
+        - docker/**
 
 github_checks:
   annotations: true