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I have upgraded my Website Publisher installation by uploading the changed files listed in the changelog, but some parts of my site no longer function.

Using the list of changed files in the Website Publisher changelog to upgrade your site is not recommended, as this is vulnerable to a number of issues, such as accidentally skipping a file, or a file mistakenly not being listed by Interspire.

The recommended method of upgrading your installation is documented in a file located at /docs/upgrade.txt

In short, to avoid any potential issue with skipped files or missing entries in the changelog, the best method of upgrading your installation is to upload all files contained in the download archive (after referring to the instructions in the upgrade.txt document to take backups of any customized files).

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