Some deprecated methods for 3rd party libraries and one for Java 17

Upgrading gradle requires upgrading to using JDK 17 (still running Jalview under Java 11).
Some deprecation warnings have been fixed in JAL-4647 but there are many that remain. The deprecation warnings remaining have been attached in a file.

These are nearly all related to the apache HttpClient and associated classes.

There is one that relates to com.sun.management.OperatingSystemMXBean.getPhysicalMemory() used in jalview/bin/MemorySetting.java. This can be fixed as there is a direct replacement (getTotalMemorySize()), but the new method doesn't exist in Java 11 so cannot be replaced yet.