fix: update theseus engine

.github/workflows/theseus-engine.yml

@@ -5,21 +5,21 @@ on:
     - cron: "0 0 1 * *"
   workflow_dispatch:
     inputs:
-      reprocess:
-        description: 'Reprocess state. Type "all" to wipe and rebuild completely, or "last" to re-calculate the most recent period.'
-        required: false
+      run_mode:
+        description: 'Run Mode (Default is Resume Run)'
+        required: true
         type: choice
         options:
-          - ""
-          - "last"
-          - "all"
-        default: ""
+          - "Resume Run (Pick up where left off)"
+          - "Complete Extraction (Wipe and rebuild all)"
+        default: "Resume Run (Pick up where left off)"
       full_fossil_scan:
         description: 'Run a full deep-scan for fossils (uncheck to only do a fast survivor update)'
         required: false
         type: boolean
         default: false
 
+
 concurrency:
   group: theseus-data-engine
   cancel-in-progress: false
@@ -72,11 +72,11 @@ jobs:
         continue-on-error: true
         env:
           REPO_NAME: ${{ matrix.repo }}
-          REPROCESS_INPUT: ${{ inputs.reprocess }}
+          RUN_MODE: ${{ inputs.run_mode }}
         run: |
           ARGS=()
-          if [ -n "$REPROCESS_INPUT" ]; then
-            ARGS+=(--reprocess "$REPROCESS_INPUT")
+          if [[ "$RUN_MODE" == "Complete Extraction (Wipe and rebuild all)" ]]; then
+            ARGS+=(--reprocess "all")
           fi
           if [ "${{ inputs.full_fossil_scan }}" != "true" ]; then
             ARGS+=(--update-survivor)

data/state/claude-code_state.json

@@ -0,0 +1 @@
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pyproject.toml

@@ -21,7 +21,7 @@ dev = [
 ]
 
 [tool.pylint]
-init-hook = "import sys; sys.path.insert(0, 'scripts')"
+init-hook = "import sys; sys.path.insert(0, '.')"
 
 [tool.pylint.format]
 max-line-length = 120

scripts/analyse_repository.py

@@ -237,8 +237,8 @@ def _filter_snapshots(
 
     :param all_periods: Full list of (period, commit) tuples.
     :param processed_periods: Set of period strings already on disk.
-    :param reprocess: Optional ``YYYY-MM`` period to force re-processing.
-    :return: List of (period, commit) tuples that need processing.
+    :param reprocess: Optional target ('all', 'last', or 'YYYY-MM') to force re-processing.
+    :return: A list of (YYYY-MM, commit_hash) tuples to process.
     """
     result: list[tuple[str, str]] = []
     for period, commit in all_periods:
@@ -415,7 +415,7 @@ def process_repository(
 
     :param repo_slug: GitHub ``owner/name`` slug.
     :param data_dir: Path to the ``data/`` output directory.
-    :param reprocess: Optional ``YYYY-MM`` period to force re-processing.
+    :param reprocess: Optional target ('all', 'last', or 'YYYY-MM') to force re-processing.
     """
     repo_name = repo_slug.split("/")[-1]
     temp_repo_path = f"./temp_workdir_{repo_slug.replace('/', '__')}"
@@ -467,7 +467,7 @@ def main() -> None:
     CLI flags
     ---------
     --repo NAME         Process only the given repository (by config name).
-    --reprocess YYYY-MM Re-process a specific snapshot period even if it already
+    --reprocess TARGET  Re-process 'all', 'last', or a specific snapshot period even if it already
                         exists on disk.
     """
     parser = argparse.ArgumentParser(
@@ -481,9 +481,9 @@ def main() -> None:
     )
     parser.add_argument(
         "--reprocess",
-        metavar="YYYY-MM",
+        metavar="TARGET",
         default=None,
-        help="Re-process a specific snapshot period (e.g. '2023-06').",
+        help="Re-process a target. Pass 'all' to wipe and rebuild, 'last' for the latest period, or a specific period like '2023-06'.",
     )
     args = parser.parse_args()
 
@@ -521,7 +521,7 @@ def main() -> None:
         logger.info("Processing %d repositories", len(selected_targets))
 
     if args.reprocess:
-        logger.info("Re-processing period: %s", args.reprocess)
+        logger.info("Re-processing target: %s", args.reprocess)
 
     max_top_level_workers = min(
         len(selected_targets),

scripts/run_pipeline.py

@@ -3,7 +3,7 @@
 
 Usage::
 
-    python -m scripts.run_pipeline [--repo NAME] [--reprocess YYYY-MM] [--update-survivor]
+    python -m scripts.run_pipeline [--repo NAME] [--reprocess TARGET] [--update-survivor]
 
 Runs all three stages in sequence on one or more repositories:
 
@@ -37,7 +37,7 @@ def run_pipeline(
     Run the full pipeline (analyse → fossils → cleanup) for all repositories.
 
     :param repo: Optional repository name to process (None = all repos).
-    :param reprocess: Optional ``YYYY-MM`` period to force re-process.
+    :param reprocess: Optional target ('all', 'last', or 'YYYY-MM') to force re-process.
     :param update_survivor: If ``True``, skip genesis scan and only refresh the
         survivor (living) fossil. Designed for monthly cron ticks.
     :return: ``True`` if any stage failed, ``False`` otherwise.
@@ -145,8 +145,8 @@ def main() -> None:
 
     CLI flags
     ---------
-    --repo NAME          Process only this repository (by config name).
-    --reprocess YYYY-MM  Re-process a specific snapshot period.
+    --repo NAME          Process only this repository.
+    --reprocess TARGET   Re-process 'all', 'last', or a specific snapshot period.
     --update-survivor    Skip genesis scan; refresh only the survivor fossil
                          (designed for monthly cron ticks).
     """
@@ -169,9 +169,9 @@ def main() -> None:
     )
     parser.add_argument(
         "--reprocess",
-        metavar="YYYY-MM",
+        metavar="TARGET",
         default=None,
-        help="Re-process a specific snapshot period (e.g. '2023-06').",
+        help="Re-process a target. Pass 'all' to wipe and rebuild, 'last' for the latest period, or a specific period like '2023-06'.",
     )
     parser.add_argument(
         "--update-survivor",