Make dexdeps multidex aware

Test: m -j32 -k dexdeps && dexdeps out/host/linux-x86/cts/android-cts/testcases/CtsLibcoreTestCases.apk
Test: verified ThreadLocal.withInitial now shown in output
Test: m -j32 cts-test-coverage
Test: verified ThreadLocal.withInitial now shown as covered in out/host/linux-x86/cts-api-coverage/test-coverage.html
Bug: 34924761
Change-Id: I19b473fb6ff47dd9f3c7321f5a2faceebc33b473
(cherry picked from commit 38e91254)