Fix handling of some global variables and clear them properly

- move make_timeout to global and add it to clear_lists()
- add _modified_files and building_base to clear_lists()

This is needed to run tests that include prepare().

cue-test.py

@@ -702,14 +702,14 @@ def test_MisspelledConfigurationGetsWarning(self):
 
 class TestSetupForBuild(unittest.TestCase):
     args = Namespace(paths=[])
-    cue.building_base = True
     if ci_os == 'windows':
         choco_installs = ['make']
         if ci_service != 'appveyor':
             choco_installs.append('strawberryperl')
         sp.check_call(['choco', 'install', '-ry'] + choco_installs)
 
     def setUp(self):
+        cue.building_base = True
         if ci_service == 'appveyor':
             os.environ['CONFIGURATION'] = 'default'
         cue.detect_context()

cue.py

@@ -163,6 +163,7 @@ def detect_context():
 setup = {}
 places = {}
 extra_makeargs = []
+make_timeout = 0.
 
 is_base314 = False
 is_make3 = False
@@ -185,6 +186,8 @@ def clear_lists():
     has_test_results = False
     silent_dep_builds = True
     do_recompile = False
+    building_base = False
+    _modified_files = set()
     ci['service'] = '<none>'
     ci['os'] = '<unknown>'
     ci['platform'] = '<unknown>'
@@ -205,8 +208,6 @@ def clear_lists():
 if 'BASE' in os.environ and os.environ['BASE'] == 'SELF':
     building_base = True
     places['EPICS_BASE'] = curdir
-else:
-    building_base = False
 
 # Setup ANSI Colors
 ANSI_RED = "\033[31;1m"