I have been struggling with the same problem and finally got it to work.
The first thing I did was to modify the default xdasconfig.properties file for the layout.ConversionPattern to not put the syslog level and time stamp and to only output the json event.
log4j.appender.R.layout.ConversionPattern=%m%n
I found through searching many posts that INDEXED_EXTRACTIONS do NOT work on indexers. INDEXED_EXTRACTIONS are applied on forwarders. From what I can tell this is something that changed in version 6. Once I put the following in the props.conf file Universal Forwarder which has the xdas log file local it started working like a charm.
props.conf on Universal Forwarder
[xdas]
INDEXED_EXTRACTIONS = json
detect_trailing_nulls = auto
SHOULD_LINEMERGE = false
Finally, modify the props.conf file on the indexer to not perform search time indexing otherwise the fields will appear to be duplicated.
props.conf on the indexer
[xdas]
KV_MODE = none
AUTO_KV_JSON = false
Hope this helps!
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