test(cli): fix typer argument parsing and scratchpad pollution

- Fixes `src/tests/test_cli_agent_mode.py` tests failing randomly when generated IDs start with a hyphen (`-`) by using `--` separator to prevent typer from misinterpreting them as options.
- Removes leftover temporary `.py` and `.md` scratchpad files that were mistakenly included in the previous commit attempt.

Co-authored-by: PR0M3TH3AN <[email protected]>

src/context/run.md

@@ -1 +0,0 @@
-Baseline reads completed by content-audit-agent.

src/decisions/run.md

@@ -1 +0,0 @@
-Update KNOWN_ISSUES and incidents.

src/test_logs/TEST_LOG_20260301.md

@@ -1,10 +0,0 @@
-
-> [email protected] validate:scheduler
-> node scripts/validate-scheduler-roster.mjs && node scripts/validate-prompt-contract.mjs && node scripts/validate-scheduler-flow-parity.mjs && npm run validate:scheduler-failure-schema
-
-Scheduler tables, roster, and prompt filenames are in sync.
-Prompt contract validated for all daily/weekly prompts.
-Scheduler flow parity validated for prompts and scheduler implementation.
-
-> [email protected] validate:scheduler-failure-schema
-> node --test test/scheduler-lock-failure-schema.contract.test.mjs

src/test_logs/run.md

@@ -1 +0,0 @@
-Logs.

src/tests/test_cli_agent_mode.py

@@ -1810,8 +1810,9 @@ def test_agent_secret_lease_issue_consume_and_exhaust(monkeypatch, tmp_path):
             "ABC123",
             "agent",
             "lease-consume",
-            lease_id,
             "--reveal",
+            "--",
+            lease_id,
         ],
     )
     assert first.exit_code == 0
@@ -1827,8 +1828,9 @@ def test_agent_secret_lease_issue_consume_and_exhaust(monkeypatch, tmp_path):
             "ABC123",
             "agent",
             "lease-consume",
-            lease_id,
             "--reveal",
+            "--",
+            lease_id,
         ],
     )
     assert second.exit_code == 1
@@ -1913,8 +1915,9 @@ def test_agent_lease_consume_hydrates_partitioned_private_entry(monkeypatch, tmp
             "ABC123",
             "agent",
             "lease-consume",
-            "lease-1",
             "--reveal",
+            "--",
+            "lease-1",
         ],
     )
     assert result.exit_code == 0

src/todo/run.md

@@ -1 +0,0 @@
-Review docs vs code.