Restructured src to more logical heirachy

cli/CLAUDE.md

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+# CLI Package
+
+Command-line interface for pathway data refresh operations.
+
+## refresh_pathways.py
+
+Main CLI module for refreshing pre-computed pathway data from Snowflake to SQLite.
+
+**Key Functions:**
+- `refresh_pathways()` — Orchestrates full pipeline: fetch from Snowflake, transform via tools/data.py, generate pathway charts, insert to SQLite
+- `insert_pathway_records()` — Bulk inserts using parameterized queries with `INSERT OR REPLACE` (handles overwrites via UNIQUE constraint)
+- `log_refresh_start()`, `log_refresh_complete()`, `log_refresh_failed()` — Tracks refresh status in pathway_refresh_log table
+- `get_default_filters()` — Loads available trusts, drugs, directories from CSV files
+
+**CLI Arguments:**
+- `--chart-type [all|directory|indication]` — Which pathway types to refresh (default: all)
+- `--dry-run` — Test without database changes
+- `--minimum-patients N` — Pathway nodes with <N patients filtered out (default: 5)
+- `-v, --verbose` — Enable debug logging
+
+**Usage:**
+```bash
+python -m cli.refresh_pathways --chart-type all
+python -m cli.refresh_pathways --chart-type indication --dry-run -v
+```
+
+**Note:** Module uses sys.path bootstrap at top to enable `python -m cli.refresh_pathways` from project root.