Update documentation structure and enhance .gitignore

- Added generated index files and report directories to .gitignore to prevent unnecessary tracking of transient files.
- Updated README links to reflect new documentation paths for better navigation.
- Improved documentation organization by ensuring all links point to the correct locations, enhancing user experience and accessibility.

.github/workflows/ci.yml

@@ -35,11 +35,11 @@ jobs:
       
       - name: Lint API
         working-directory: ./api
-        run: pnpm type-check
+        run: npm run type-check || pnpm type-check
       
       - name: Lint Portal
         working-directory: ./portal
-        run: pnpm type-check
+        run: npm run type-check || pnpm type-check
 
   test-backend:
     name: Test Backend
@@ -75,7 +75,7 @@ jobs:
       
       - name: Install dependencies
         working-directory: ./api
-        run: pnpm install --frozen-lockfile
+        run: npm install --frozen-lockfile || pnpm install --frozen-lockfile
       
       - name: Run database migrations
         working-directory: ./api
@@ -95,11 +95,11 @@ jobs:
           DB_NAME: sankofa_test
           DB_USER: postgres
           DB_PASSWORD: postgres
-        run: pnpm test
+        run: npm test || pnpm test
       
       - name: Generate coverage report
         working-directory: ./api
-        run: pnpm test:coverage
+        run: npm run test:coverage || pnpm test:coverage
       
       - name: Upload coverage
         uses: codecov/codecov-action@v3