feat: restructure as PyPI package with src layout

Reorganize the project into a proper Python package installable via
`pip install chunksilo`, while keeping GitHub release bundles intact.

- Move source files into src/chunksilo/ (src layout)
- Split chunksilo.py into search.py (core pipeline) + server.py (MCP wrapper)
- Add cli.py with `search_docs` console_scripts entry point
- Make confluence support optional via `pip install chunksilo[confluence]`
- Use requirements.txt as single source of truth for dependencies (dynamic)
- Update all tests, CI workflows, and bundle scripts for new structure
- Add PyPI publish job to manual-release workflow

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: Chetic

.github/workflows/manual-release.yml

@@ -259,4 +259,25 @@ jobs:
           gh api "repos/$GITHUB_REPOSITORY/actions/artifacts" --paginate -q '.artifacts[].id' | while read -r ARTIFACT_ID; do
             echo "Deleting artifact $ARTIFACT_ID"
             gh api "repos/$GITHUB_REPOSITORY/actions/artifacts/$ARTIFACT_ID" -X DELETE
-          done
+          done
+
+  publish_pypi:
+    needs: release
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Build package
+        run: |
+          pip install build
+          python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/test-functional.yml

@@ -23,8 +23,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install -r requirements.txt
-          python -m pip install -r test/requirements.txt
+          python -m pip install -e ".[confluence,test]"
 
       - name: Check dependency licenses
         run: |
@@ -43,6 +42,7 @@ jobs:
           /tmp/license-check-venv/bin/pip install --quiet --upgrade pip
           /tmp/license-check-venv/bin/pip install --quiet \
             -r requirements.txt \
+            "llama-index-readers-confluence>=0.6.0,<1" \
             -c scripts/manylinux_2_34-constraints.txt
           /tmp/license-check-venv/bin/pip install --quiet pip-licenses
           /tmp/license-check-venv/bin/pip-licenses --partial-match \
@@ -57,7 +57,7 @@ jobs:
           DATA_DIR: ./test_data_dummy
           STORAGE_DIR: ./test_storage_dummy
         run: |
-          python index.py --download-models
+          python -m chunksilo.index --download-models
 
       - name: Run all functional tests
         env:

.github/workflows/test-rag-metrics.yml

@@ -26,8 +26,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install -r requirements.txt
-          python -m pip install -r test/requirements.txt
+          python -m pip install -e ".[confluence,test]"
 
       - name: Run RAG metrics test suite
         env: