build: embed test scripts into org files and purge tests directory

- Embedded run-all-tests.lisp into harness/package.org.
- Deleted the tests/ directory and orphaned Python test scripts, as all other test files are correctly tangled from their parent org files.

tests/tool-permissions-tests.lisp

@@ -1,34 +0,0 @@
-(defpackage :opencortex-tool-permissions-tests
-  (:use :cl :fiveam :opencortex)
-  (:export #:tool-permissions-suite))
-
-(in-package :opencortex-tool-permissions-tests)
-
-(def-suite tool-permissions-suite
-  :description "Tests for Tool Permissions skill")
-
-(in-suite tool-permissions-suite)
-
-(test default-permission-is-allow
-  "Verify default permission is :allow."
-  (is (eq (get-tool-permission "unknown-tool") :allow)))
-
-(test set-and-get-permission
-  "Verify setting and getting permissions."
-  (set-tool-permission "test-tool-abc" :deny)
-  (is (eq (get-tool-permission "test-tool-abc") :deny)))
-
-(test permission-gate-allow
-  "Verify :allow tier passes through."
-  (set-tool-permission "gate-allow-tool" :allow)
-  (is (eq (check-tool-permission-gate "gate-allow-tool" nil) :allow)))
-
-(test permission-gate-deny
-  "Verify :deny tier blocks."
-  (set-tool-permission "gate-deny-tool" :deny)
-  (is (eq (check-tool-permission-gate "gate-deny-tool" nil) :deny)))
-
-(test permission-gate-ask
-  "Verify :ask tier returns ask list."
-  (set-tool-permission "gate-ask-tool" :ask)
-  (is (listp (check-tool-permission-gate "gate-ask-tool" nil))))