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Can I index partially today and the rest tomorrow?
Of course, you control the indexing process; however you'll have to find a way to define were to stop and then restart at same position.
You could also leave it running, you can stil use an application while it's indexing.
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do I have to get the commit instruction to save the created indexes?
When using the index() API the Lucene backend will flush some indexed documents periodically, so you don't have to wait for commit() to see something in the index, but without guarantees. If you need to be sure all entities you indexed are flushed to the index you have to commit. This shouldn't be a problem as you control the commit() yourself. In 3.1.0 there is a "flushToIndexes()" method; you'll have to upgrade to have more control.
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how can I study the Lucene? files they are all binary.
Look for Luke in the FAQ
http://www.hibernate.org/446.html .