This is a MASSIVE update done all by @mbaxter. It makes things much better as you can read below

/f perms is now granted by default, as it is the standard way to manage faction access.
You can now use the default_permissions.conf file to manage the default state.
Some config entries no longer exist and are controlled by /f perms now
Most commands that required a certain rank, now can be controlled by /f perms instead (default /f perms are set to the old command rank)
Importantly, you can now LOCK any /f perms permission to control which can be modified by players.
Introduced some new /f perms permissions.
Support for online/offline separation of /f perms (optional, turned off by default)
Temporarily removed customizability of the GUI. It will return in a future update.
Warp GUI now supports any number of warps.

Start of moving all config to new files in a new config folder.
First to go, conf.json is migrated to config/main.conf
New default /f perms config in config folder
Factions data is now stored in a "data" folder

New command /f warpother
If a faction grants the /f perms WARP permission to faction relations (e.g. allies), they can visit that faction's warps.
(Of course, by default this isn't the case)
Includes GUI support.

New command /f delhome

Greatly improved piston interactions, if preventing pistons across faction borders.

Re-added support for {group} across placeholder usage.

Temporarily removed dynmap integration as it was partly broken. Will return soon.

Internal code changes which may break compatibility with plugins that hook into Factions.

Border explosions, if prevented via config, now properly obey restrictions
For example, properly protecting safezone from exploding by a creeper just outside it.

Added update checker.

Added debug command to help us better provide support.

Made the anti-duping exploit feature configurable rather than always enabled.

Added config option to remove whitespace from data storage to save space.

Fixed world border detection issues
Added some missed items to various protection lists.
General code improvements for performance.
No longer incorrectly outputs balance for invalid /f top
By default no longer shows [4-] for factionless players.
Added relationship color to /f map legend
Fixes bug where player was marked as flying but wasn't flying.
Fix slowdown under certain circumstances when other placeholder plugins were present.
No longer send players outside the border with /f stuck
Fix bug with LWC integration that could cause an error.