In your Sycamore directory (inside of sycamore_base) you'll find a file called maintenance.py. Running python maintenance.py will present with you a few options. We outline a bit of detail on each here.
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Rebuilding page caches is important to do if you change the relative_dir setting in your configuration. If you change relative_dir then select the option to "rebuild all page caches".
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Rebuilding the search index will go through each page in your wiki and add it to a fresh Xapian database. You should run this step if you turned on Xapian after running the initial install script or if you want to rebuild the search index for any other reason.
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Rebuilding "only outdated page caches" is useful to do in certain cases. The explaination is a bit technical so feel free to skip it: Sometimes things "expire" but do not get rebuilt. This happens very infrequently, but is sometimes unavoidable in cases such as many pages doing an [[Include()]] of another page. When the included page is edited we do not rebuild all the pages that include that page; instead, we expire all of those pages' caches. People will never see outdated pages, but this means that the link information won't be updated until somebody visits the expired page. This behavior may change in the future.
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If you are running your Sycamore server in FastCGI mode, you may have to restart the webserver for your changes to take effect.