Refactor codebase into core and server subpackages

- Moved shared logic (config, exceptions, ignore_patterns, etc.) into `core/`.
- Created `server/` to host FastAPI modules, static files, and templates.
- Updated import paths for CLI and tests to reference `core.*` and `server.*`.
- Changed static references from `"/static"` to `"/server/static"` and templates from `"/templates"` to `"/server/templates"`.
- Adjusted references in `base.jinja`, `server/main.py`, `server/query_processor.py`, and routers to reflect the new server paths.
- Ensured Docker builds now correctly serve static and template files from `server/`.

Author: filipchristiansen

Dockerfile

@@ -41,4 +41,4 @@ USER appuser
 
 EXPOSE 8000
 
-CMD ["python", "-m", "uvicorn", "main:app", "--host", "0.0.0.0", "--port", "8000"]
+CMD ["python", "-m", "uvicorn", "server.main:app", "--host", "0.0.0.0", "--port", "8000"]

src/core/__init__.py

@@ -6,7 +6,7 @@
 from pathlib import Path
 from typing import Any
 
-from gitingest.exceptions import InvalidNotebookError
+from core.exceptions import InvalidNotebookError
 
 
 def process_notebook(file: Path, include_output: bool = True) -> str:

src/config.py src/core/config.pysrc/config.py renamed to src/core/config.py

@@ -6,15 +6,10 @@
 
 import tiktoken
 
-from config import MAX_DIRECTORY_DEPTH, MAX_FILES, MAX_TOTAL_SIZE_BYTES
-from gitingest.exceptions import (
-    AlreadyVisitedError,
-    InvalidNotebookError,
-    MaxFileSizeReachedError,
-    MaxFilesReachedError,
-)
-from gitingest.notebook_utils import process_notebook
-from gitingest.query_parser import ParsedQuery
+from core.config import MAX_DIRECTORY_DEPTH, MAX_FILES, MAX_TOTAL_SIZE_BYTES
+from core.exceptions import AlreadyVisitedError, InvalidNotebookError, MaxFileSizeReachedError, MaxFilesReachedError
+from core.notebook_utils import process_notebook
+from core.query_parser import ParsedQuery
 
 
 def _should_include(path: Path, base_path: Path, include_patterns: set[str]) -> bool:

src/gitingest/exceptions.py src/core/exceptions.pysrc/gitingest/exceptions.py renamed to src/core/exceptions.py

@@ -9,10 +9,10 @@
 from pathlib import Path
 from urllib.parse import unquote, urlparse
 
-from config import MAX_FILE_SIZE, TMP_BASE_PATH
-from gitingest.exceptions import InvalidPatternError
-from gitingest.ignore_patterns import DEFAULT_IGNORE_PATTERNS
-from gitingest.repository_clone import _check_repo_exists, fetch_remote_branch_list
+from core.config import MAX_FILE_SIZE, TMP_BASE_PATH
+from core.exceptions import InvalidPatternError
+from core.ignore_patterns import DEFAULT_IGNORE_PATTERNS
+from core.repository_clone import _check_repo_exists, fetch_remote_branch_list
 
 HEX_DIGITS: set[str] = set(string.hexdigits)
 
@@ -227,7 +227,7 @@ async def _configure_branch_and_subpath(remaining_parts: list[str], url: str) ->
         # Fetch the list of branches from the remote repository
         branches: list[str] = await fetch_remote_branch_list(url)
     except RuntimeError as e:
-        warnings.warn(f"Warning: Failed to fetch branch list: {e}")
+        warnings.warn(f"Warning: Failed to fetch branch list: {e}", UserWarning)
         return remaining_parts.pop(0)
 
     branch = []

src/gitingest/ignore_patterns.py src/core/ignore_patterns.pysrc/gitingest/ignore_patterns.py renamed to src/core/ignore_patterns.py

@@ -3,7 +3,7 @@
 import asyncio
 from dataclasses import dataclass
 
-from gitingest.utils import async_timeout
+from core.utils import async_timeout
 
 TIMEOUT: int = 20
 

src/gitingest/notebook_utils.py src/core/notebook_utils.pysrc/gitingest/notebook_utils.py renamed to src/core/notebook_utils.py

@@ -4,10 +4,10 @@
 import inspect
 import shutil
 
-from config import TMP_BASE_PATH
-from gitingest.query_ingestion import run_ingest_query
-from gitingest.query_parser import ParsedQuery, parse_query
-from gitingest.repository_clone import CloneConfig, clone_repo
+from core.config import TMP_BASE_PATH
+from core.query_ingestion import run_ingest_query
+from core.query_parser import ParsedQuery, parse_query
+from core.repository_clone import CloneConfig, clone_repo
 
 
 async def ingest(