chore: prune unused imports and duplicate import redefinitions

Remove unused imports (F401) and duplicate/shadowed import
redefinitions (F811) across the codebase using ruff's safe
autofixes. No behavioral changes -- imports only.

- ~1400 safe autofixes applied across 644 files (net -1072 lines)
- __init__.py re-exports preserved (excluded from F401 removal so
  public re-export surfaces stay intact)
- Re-exports that are imported or monkeypatched by tests but look
  unused in their defining module are kept with explicit # noqa:
  F401 (gateway/run.py load_dotenv; run_agent re-exports from
  agent.message_sanitization, agent.context_compressor,
  agent.retry_utils, agent.prompt_builder, agent.process_bootstrap,
  agent.codex_responses_adapter)
- Unsafe F841 (unused-variable) fixes deliberately skipped -- those
  can change behavior when the RHS has side effects
- ruff lints remain disabled in pyproject.toml (only PLW1514 is
  selected); this is a one-time cleanup, not a config change

Verification:
- python -m compileall: clean
- pytest --collect-only: all 27161 tests collect (zero import errors)
- core entry points import clean (run_agent, model_tools, cli,
  toolsets, hermes_state, batch_runner, gateway)
- static scan: every name any test imports directly from an edited
  module still resolves

optional-skills/research/drug-discovery/scripts/chembl_target.py

@@ -5,7 +5,7 @@ Usage: python3 chembl_target.py "EGFR" --min-pchembl 7 --limit 20
 No external dependencies.
 """
 import sys, json, time, argparse
-import urllib.request, urllib.parse, urllib.error
+import urllib.request, urllib.parse
 
 BASE = "https://www.ebi.ac.uk/chembl/api/data"
 

optional-skills/research/drug-discovery/scripts/ro5_screen.py

@@ -4,8 +4,8 @@ ro5_screen.py — Batch Lipinski Ro5 + Veber screening via PubChem API.
 Usage: python3 ro5_screen.py aspirin ibuprofen paracetamol
 No external dependencies beyond stdlib.
 """
-import sys, json, time, argparse
-import urllib.request, urllib.parse, urllib.error
+import sys, json, time
+import urllib.request, urllib.parse
 
 BASE = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name"
 PROPS = "MolecularWeight,XLogP,HBondDonorCount,HBondAcceptorCount,RotatableBondCount,TPSA"

optional-skills/research/osint-investigation/scripts/fetch_gdelt.py

@@ -11,7 +11,6 @@ from __future__ import annotations
 
 import argparse
 import csv
-import json
 import sys
 import time
 import urllib.parse

optional-skills/research/osint-investigation/scripts/fetch_opencorporates.py

@@ -12,7 +12,6 @@ from __future__ import annotations
 
 import argparse
 import csv
-import json
 import os
 import re
 import sys

optional-skills/research/osint-investigation/scripts/fetch_wikipedia.py

@@ -12,7 +12,6 @@ from __future__ import annotations
 
 import argparse
 import csv
-import json
 import re
 import sys
 import urllib.parse

optional-skills/research/osint-investigation/scripts/timing_analysis.py

@@ -19,7 +19,6 @@ import argparse
 import csv
 import datetime as dt
 import json
-import math
 import random
 import statistics
 from collections import defaultdict