ISPN-3560 Size after a suspended transaction is resumed is incorrectly
calculated

* Fixed EntrySet, KeySet, Values and Size commands to count context
values except if they were removed to be more consistent with what
data is available to the user

* Also fixed LockingTest by adding eventually to prevent random failure
ISPN-3563 Some logging methods in Infinispan Core at error level are missing the ID
ISPN-3563 Some logging methods in Infinispan Core at warn level are missing the ID
ISPN-3563 Fix typos in log method names
ISPN-2815 Put to Transactional cache with enabled indexing to InfinispanDirectory doesn't work properly

* Re-enable and add test
ISPN-2815 Put to Transactional cache with enabled indexing to InfinispanDirectory doesn't work properly
ISPN-3151 Disable transaction table completed transactions cleanup service when total order is used
ISPN-3285 Remove dependency to Lucene Analyzers

These were already optional and not really used, so it's probably best to remove them.
ISPN-2967 Preload fails when auto-commit is false for tx caches
ISPN-3349 Avoid CDI module depending on JCache module

* CDI now works independent from the JCache module.
* Removed classes ported from solder that are no longer needed.
ISPN-3578 Missing component metadata in extended statistics module
ISPN-1089 NullPointerException when using an AtomicMap without a TransactionManagerLookup setup
ISPN-3581 Hide all non-API classes and methods from package org.infinispan.query
ISPN-3580 Methods setTimeoutExceptionFactory and registerKeyTransformer on SearchManager should not be public API
ISPN-3579 Upgrade to HQL Parser 1.0.0.Alpha5 and avoid dependency on custom built ANTLR release
CDI dependency on infinispan-server-core should be scoped to test
Fix a few compile warnings and deprecations
ISPN-3221 NPE in MapReduceTask reduce phase

Remove lifespan and maxIdle settings, and enable state transfer in the
default M/R intermediate cache configuration,
ISPN-3557 Key set not empty after transactional CACHE_MODE_LOCAL flagged clear

* Added tests to make sure issue is fixed
* This problem was fixed in ISPN-3560
ISPN-2797 Do not allow indexing on a cache in Invalidation mode