Gmail – Filtering subjects with NOT(-)

This is by design, so it is not possible. There is no mechanism to merge conversations and the only way to split a conversation is to change the subject, even if it's only one character.

In Gmail create a filter:
1. In "Create Filter" write into Subject: -[digester] and into "Has the words" write list:user@commons.apache.org (depending to which list you are subscribed to)
2. In the next step select "Delete it"
This will delete all mails received from the mailing list that do not contain [digester] in the subject the moment they arrive into your inbox.

UPDATE: I couldn't find a way to filter by In-Reply-To or References email header used by the mailing list to create threads but you could try something like this: list:user@commons.apache.org (subject:(-[digester]) OR -your_email@gmail.com)
This will keep also mails that contain your email address somewhere and so are likely to be replies to you.