chore: untrack two committed store files, add the rules that let them in

.env.d.examples/00_crossref-local.env

@@ -11,5 +11,5 @@ CROSSREF_LOCAL_API_URL=http://localhost:31291
 CROSSREF_LOCAL_HOST=0.0.0.0
 CROSSREF_LOCAL_PORT=31291
 
-# Path to SQLite database (for db mode)
+# Path to the local CrossRef database file (for db mode)
 # CROSSREF_LOCAL_DB=/path/to/crossref.db

.gitignore

@@ -147,6 +147,15 @@ local_settings.py
 db.sqlite3
 db.sqlite3-journal
 
+# Embedded database files. These are binary, so `git grep` skips them and a
+# committed one stays invisible until something opens it. Two were already
+# tracked here (a clew runtime store and a legacy example's) before these
+# rules existed; the rules are what stop the next one.
+**/*.sqlite
+**/*.sqlite3
+**/clew.db
+.scitex/clew/runtime/
+
 # Flask stuff:
 instance/
 .webassets-cache

docs/sphinx/core_concepts.rst

@@ -37,7 +37,7 @@ The Session Model
 2. **Logging**: All stdout/stderr captured to ``script.log``
 3. **Config injection**: YAML files from ``./config/`` merged and injected
 4. **CLI generation**: Function parameters become ``--flags``
-5. **Provenance**: File hashes recorded to SQLite for reproducibility
+5. **Provenance**: File hashes recorded to the Clew store for reproducibility
 
 .. code-block:: python
 
@@ -124,7 +124,8 @@ Provenance Tracking (Clew)
 --------------------------
 
 Inside ``@stx.session``, every ``stx.io.save`` and ``stx.io.load`` call
-records the file's SHA-256 hash to a local SQLite database. This enables:
+records the file's SHA-256 hash to the Clew provenance store. This
+enables:
 
 - **Verification**: Check if output files have been modified since creation
 - **DAG reconstruction**: Trace which inputs produced which outputs

docs/sphinx/modules/io.rst

@@ -94,7 +94,7 @@ Provenance Tracking
 -------------------
 
 Inside ``@stx.session``, every ``save`` and ``load`` records file hashes
-to a local SQLite database for reproducibility verification.
+to the Clew provenance store for reproducibility verification.
 
 .. code-block:: python
 

pyproject.toml

@@ -792,7 +792,7 @@ web = [
 
 # Clew Module - Hash-based verification for reproducible science (Ariadne's thread)
 # Use: pip install scitex[clew]
-# Note: No extra dependencies - uses only stdlib (sqlite3, hashlib)
+# Note: clew owns its own store; nothing extra is pulled in here.
 clew = ["scitex-clew==0.17.0"]
 
 # Writer Module - Academic paper writing

tests/integration/test_cross_package_imports.py

@@ -165,7 +165,6 @@
     "scitex_io._load_modules._pandas",
     "scitex_io._load_modules._pdf",
     "scitex_io._load_modules._pickle",
-    "scitex_io._load_modules._sqlite3",
     "scitex_io._load_modules._torch",
     "scitex_io._load_modules._txt",
     "scitex_io._load_modules._xml",