Bugfix/backend fixes and test suite stabilization

.continue/models/new-model.yaml

@@ -0,0 +1,11 @@
+name: New model
+version: 0.0.1
+schema: v1
+models:
+  - provider: anthropic
+    model: claude-3-7-sonnet-latest
+    apiKey: ${{ secrets.ANTHROPIC_API_KEY }}
+    name: Claude 3.7 Sonnet
+    roles:
+      - chat
+      - edit

.continue/prompts/new-prompt.yaml

@@ -0,0 +1,8 @@
+name: New prompt
+version: 0.0.1
+schema: v1
+prompts:
+  - name: New prompt
+    description: New prompt
+    prompt: Please write a thorough suite of unit tests for this code, making sure
+      to cover all relevant edge cases

.continue/rules/new-rule.yaml

@@ -0,0 +1,5 @@
+name: New rule
+version: 0.0.1
+schema: v1
+rules:
+  - Always give concise responses

.flake8

@@ -0,0 +1,4 @@
+[flake8]
+max-line-length = 100
+exclude = .git,__pycache__,build,dist
+ignore = E203, W503

.github/workflows/README.md

@@ -0,0 +1,61 @@
+# GitHub Actions Workflows
+
+This directory contains GitHub Actions workflows for the EmailIntelligence project.
+
+## Workflows
+
+### 1. CI Workflow (`ci.yml`)
+- **Trigger**: Push to `main` or `scientific` branches, and pull requests targeting these branches
+- **Purpose**: Runs comprehensive tests, linting, and type checking for all code changes
+- **Features**:
+  - Python 3.11 testing
+  - pytest with coverage reporting
+  - Code formatting checks (black, isort)
+  - Linting (flake8)
+  - Type checking (mypy)
+
+### 2. Dependabot Auto-Merge (`dependabot-auto-merge.yml`)
+- **Trigger**: Pull requests opened, synchronized, or reopened
+- **Purpose**: Automatically merges Dependabot pull requests when CI passes
+- **Safety Features**:
+  - Only runs for PRs created by `dependabot[bot]`
+  - Uses GitHub's native PR status checks (no bash JSON parsing)
+  - Waits for CI workflow completion before proceeding
+  - Verifies PR is mergeable and not in draft state using GitHub context
+  - Comprehensive error handling for GitHub CLI operations
+  - Adds approval comment before enabling auto-merge
+  - Uses GitHub's auto-merge feature for safety
+
+## Security Considerations
+
+The Dependabot auto-merge workflow includes several safety measures:
+1. **Identity Verification**: Only runs for PRs from `dependabot[bot]`
+2. **CI Dependency**: Waits for and requires CI workflow success
+3. **Native GitHub Checks**: Uses GitHub's built-in PR status instead of fragile parsing
+4. **Merge Readiness**: Verifies PR is in a mergeable state using GitHub context
+5. **Error Handling**: Comprehensive error handling with graceful degradation
+6. **Approval Process**: Automatically approves and adds explanatory comment
+
+## Setup Requirements
+
+For the workflows to function properly, ensure:
+1. The repository has the necessary permissions for GitHub Actions
+2. The `GITHUB_TOKEN` has sufficient permissions for auto-merge operations
+3. Branch protection rules (if any) are compatible with auto-merge
+4. All dependencies are properly defined in `pyproject.toml`
+
+## Customization
+
+To modify the auto-merge behavior:
+- Edit the conditions in the workflow `if` statement (line 15)
+- Adjust the CI check name in the `wait-for-check` action (line 23)
+- Modify the merge strategy (currently uses `--merge`, could use `--squash` or `--rebase`)
+- Change timeout values for CI wait (currently 600 seconds)
+
+## Architecture Improvements
+
+The workflows have been optimized for:
+- **Reliability**: Native GitHub API usage instead of bash JSON parsing
+- **Simplicity**: Single-purpose jobs without unnecessary complexity
+- **Error Handling**: Comprehensive error checking with graceful degradation
+- **Performance**: Eliminates duplicate test runs by trusting CI results

.github/workflows/ci.yml

@@ -0,0 +1,43 @@
+name: CI
+
+on:
+  push:
+    branches: [ main, scientific ]
+  pull_request:
+    branches: [ main, scientific ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          version: "latest"
+
+      - name: Install dependencies
+        run: |
+          uv sync --dev
+
+      - name: Run tests
+        run: |
+          uv run pytest backend/ -v --tb=short --cov=backend --cov-report=xml
+
+      - name: Run linting
+        run: |
+          uv run flake8 backend/
+          uv run black --check backend/
+          uv run isort --check-only backend/
+
+      - name: Type checking
+        run: |
+          uv run mypy backend/ --show-error-codes --no-strict-optional

.github/workflows/dependabot-auto-merge.yml

@@ -0,0 +1,54 @@
+name: Dependabot Auto-Merge
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+
+permissions:
+  contents: write
+  pull-requests: write
+  checks: read
+
+jobs:
+  auto-merge:
+    runs-on: ubuntu-latest
+    if: github.actor == 'dependabot[bot]' && github.event.pull_request.mergeable_state == 'clean' && !github.event.pull_request.draft
+
+    steps:
+      - name: Wait for CI checks to complete
+        uses: fountainhead/action-wait-for-check@v1.2.0
+        id: wait-for-ci
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          checkName: test
+          ref: ${{ github.event.pull_request.head.sha }}
+          timeoutSeconds: 600
+          intervalSeconds: 10
+
+      - name: Auto-merge Dependabot PR
+        if: steps.wait-for-ci.outputs.conclusion == 'success'
+        run: |
+          set -e
+          echo "CI checks passed. Auto-merging Dependabot PR #${{ github.event.pull_request.number }}"
+
+          # Approve the PR first
+          if ! gh pr review ${{ github.event.pull_request.number }} --approve --body "✅ CI checks passed! Auto-merging this Dependabot PR."; then
+            echo "Failed to approve PR. Exiting."
+            exit 1
+          fi
+
+          # Enable auto-merge
+          if ! gh pr merge --auto --merge ${{ github.event.pull_request.number }}; then
+            echo "Failed to enable auto-merge. Checking if already enabled..."
+            # Check if auto-merge is already enabled
+            if gh pr view ${{ github.event.pull_request.number }} --json autoMergeRequest --jq '.autoMergeRequest' | grep -q "null"; then
+              echo "Auto-merge failed and is not enabled. Manual intervention required."
+              exit 1
+            else
+              echo "Auto-merge is already enabled."
+            fi
+          fi
+
+          echo "Auto-merge successfully enabled for PR #${{ github.event.pull_request.number }}"
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -1,45 +1,87 @@
-jsons
-node_modules
-dist
+# General
 .DS_Store
-server/public
+Thumbs.db
+generated-icon.png
+
+# Logs
+logs/
+*.log
+
+# Node / frontend
+node_modules/
+dist/
 vite.config.ts.*
-*.tar.gz
-.vscode/settings.json
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+pnpm-lock.yaml
+package-lock.json
+uv.lock
+
+# Python caches and artifacts
+__pycache__/
+*.py[cod]
+*$py.class
+.pytest_cache/
+.mypy_cache/
+.cache/
+htmlcov/
 
-# Python virtual environment created by launch.py
+# Virtual environments
 venv/
+.venv/
+env/
+ENV/
+.Python
+
+# Environment & secret files
 .env
 .env.*
-*.env
 !.env.example
-jsons/*
 token.json
 credentials.json
+apikey.json
 
-# Ignore configuration and local environment files
-*.local.config
-*.local.json
-*.local.yaml
-*.local.yml
-config.local.*
+# Build / packaging
+build/
+dist/
+*.egg-info/
+pip-wheel-metadata/
+*.egg
+*.whl
 
-# Ignore hidden files and directories, except for specific exceptions
-.*
-!docs/.gitkeep
+# Databases
+*.sqlite3
+*.db
+*.db-journal
 
-# Ignore Python cache and diagnostic files
-__pycache__/
+# Coverage
+.coverage
+.coverage.*
+coverage.xml
+coverage/
+*.cover
+
+# IDEs / editors
+.vscode/
+.vscode/settings.json
+.idea/
+*.iml
+*.sublime-project
+*.sublime-workspace
+.history
+
+# Misc
 diagnosis_message.txt
-# Ignore config files generated by local runs
 *.local.config
 *.local.json
 *.local.yaml
 *.local.yml
 config.local.*
+config/*.local.*
 
-# Ignore all dotfiles (hidden files)
-.*
+# Keep the docs placeholder
 !docs/.gitkeep
-__pycache__/
-diagnosis_message.txt
+
+# Ignore the jsons folder which may contain local data/secrets
+jsons/