Put the coverage data files in the reports dir, where they will be treated like the disposable things they are.

cms/.coveragerc

@@ -1,6 +1,6 @@
 # .coveragerc for cms
 [run]
-data_file = cms/.coverage
+data_file = reports/cms/.coverage
 
 [report]
 ignore_errors = True

common/lib/capa/.coveragerc

@@ -1,6 +1,6 @@
 # .coveragerc for common/lib/capa
 [run]
-data_file = common/lib/capa/.coverage
+data_file = reports/common/lib/capa/.coverage
 
 [report]
 ignore_errors = True

common/lib/xmodule/.coveragerc

@@ -1,6 +1,6 @@
 # .coveragerc for common/lib/xmodule
 [run]
-data_file = common/lib/xmodule/.coverage
+data_file = reports/common/lib/xmodule/.coverage
 
 [report]
 ignore_errors = True

lms/.coveragerc

@@ -1,6 +1,6 @@
 # .coveragerc for lms
 [run]
-data_file = lms/.coverage
+data_file = reports/lms/.coverage
 
 [report]
 ignore_errors = True

rakefile

@@ -209,10 +209,10 @@ namespace :coverage do
             sh("coverage xml -o reports/#{dir}/coverage.xml --rcfile=#{dir}/.coveragerc")
         end
     end
-end
 
-TEST_TASK_DIRS.each do |dir|
-    CLOBBER.include("#{dir}/.coverage")
+    TEST_TASK_DIRS.each do |dir|
+        CLOBBER.include("#{dir}/.coverage")
+    end
 end
 
 task :runserver => :lms