Re-enable linting

We were currently ignoring both deprecation and serial warnings. This
prevents warnings during the build, but hides useful information about
code that could/should be changed for all sorts of reasons.

In some instances of such warnings, the appropriate action is already
being taken (e.g. StorageUtils), so instead of ignoring all warnings, we
can just add a @SuppressWarnings("deprecation") in the appropriate
methods. Others scenarios will require more effort, like replacing
ProgressDialogs with something else. Let's re-enable the lint warnings
and work our way through them.

Closes: #3273

build.gradle

@@ -19,7 +19,7 @@ allprojects {
 
     gradle.projectsEvaluated {
         tasks.withType(JavaCompile) {
-            options.compilerArgs << "-Xlint" << "-Xlint:-deprecation" << "-Xlint:-serial"
+            options.compilerArgs << "-Xlint"
         }
     }
 }