If you are using GLI, you need to select "Minimal Rebuild" on the Create Pane.
If you are building on the command line, you can use incremental-rebuild.pl, incremental-import.pl and incremental-buildcol.pl in place of full-rebuild.pl, import.pl and buildcol.pl.
Incremental importing: New documents will be imported. Modified documents will be re-imported. Deleted documents will be removed from the collection. If metadata has changed, then documents will be reimported.
Important note for collection design: GLI can notice that metadata in a folder has been added/changed, but it is not smart enough to tell which documents in the folder have changed metadata. Therefore, if metadata in a folder has changed (including new metadata being added), then all documents in that folder will be reimported. This means that if you have all your documents in the top level import folder, adding new metadata or changing any metadata for any document will result in all documents being reimported. If you intend to do incremental import, then please organize your documents into subfolders. That way modifying metadata for some documents won't result in all other documents being reimported.
Incremental indexing: Currently only the Lucene indexer can do incremental indexing. If you are using MG/MGPP then a full buildcol pass will be done, even if incremental-buildcol.pl is used.
If collection design has changed, then you will need to do a full rebuild. Changes to plugin options, and some import options will necessitate a full import. Changes to search indexes, partition indexes, browsing classifiers will necessitate a full buildcol.
Note, changes on the Format pane do not require a rebuild at all.
See this page for some information about the code involved with incremental building.