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I have dedicated 5GB of space for my home folder. I have 6 email boxes and when I add them to Thunderbird it downloads everything from them and fills up the whole home folder (3-4GB). This is unacceptable. I need to be able to limit its cache, I don't need all of the emails downloaded, just the new ones. I tried setting lower space at Edit -> Preferences -> Advanced -> Network & Disk space but it does not work, it again downloads 3-4GB of messages...

How do I limit it to 100-200MB?

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It doesn't limit to 100-200 MB, but you can change the settings to only download the newest messages.

Go to Edit -> Account Settings -> Synchronization & Storage
under the "Disk Space" heading, select
"Synchronize Most recent" & "Don't Download Messages Larger Than", then input your desired values.

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However, checking this option doesn't seem to clear the mails that were already downloaded? – JI Xiang Jan 7 at 10:31

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