I know about $SPLUNK_HOME/etc/system/local/inputs.conf and using wildcards to minimize the amount of stanzas in it. I'd like to know if its somehow possible to define some kind of inpus.conf.d directory and have one inputs.conf-like file for every log we would like to monitor.
Our current inputs.conf is autogenerated and quite "messy". Having a directory with a dozen or so config files could be better and more clearly arranged.
Depending on how you generate the inputs.conf, you might consider creating the separate configurations under $SPLUNK_HOME/etc/apps/.
You would create a series of sub-directories to this, by whatever means you wanted to delineate, under those you would have "default" or "local" subdirectories, and in those you would have fragmentary files similar in content to the files you would normally find under etc/default or etc/local, which in your case would be stanzas from inputs.conf, e.g.