Thank you for your review.

* Neat URL is good but lacks dealing with redirects (including nested ones) and retrieving long URLs from shortened URLs.
That's why there exist other addons that do exactly that. I believe Neat URL should do one thing well, which is "cleaning URLs". Skipping redirects or retrieving long URLs from short ones will not be in the feature scope of Neat URL.

* Adding a new rule to the bottom on a new line caused the addon to not use the line.
I don't consider this to be a high priority issue. Might be improved in a later version.

* Using $.html@phys.org $html@phys.org or $.html@phys.* or $html@phys.* caused the extension to remove the html part from the link. Plz Fix.
Sorry, this is expected behaviour and working as intended. $ removes everything that comes after it when used as a Neat URL parameter.