Achtung Spoiler:
New modding options: Details regarding these changes can be found here.

Bugs fixed

Nessus Mining Stations could reduce ecological damage in bases without aerospace complexes. Fixed in patch version 1.1.
Tree Farms, Hybrid Forests, Centauri Preserves, and Temples of Planet would count as fungal pops for purposes unrelated to calculating ecological damage chance, such as determining when ecological damage would begin to produce mind worms and global warming. Fixed in patch version 1.1
Echelon mirrors could (rarely) cause crashes or incorrect display of a tile's energy output; this has been fixed in version 1.3.
The unit cost formula would sometimes incorrectly apply an extra cost for using two special abilities even when one was free; this has been fixed in version 1.3.
In patch version 2.0 and later, the effect on clean minerals of Tree Farms, Hybrid Forests, Centauri Preserves, and Temples of Planet is based on the number owned, not the number that have been built. It still will not apply until the first fungal pop.
Setting retool strictness equal to 3 would fail to work (it would work as retool strictness 2); this has been fixed as of version 2.0.
Native life will no longer examine major atrocities and tectonic missiles separately when determining aggressiveness; everything that creates extra ecological damage is treated as identical.
When determining whether there were enough nonspecialists to become talents and drones (to cancel talents with drones if there aren't enough), superdrones would be counted twice. This has been fixed as of version 2.1.
The drone reduction effect of the Planetary Transit system was marked as a facility effect rather than a project effect; this has been fixed as of version 2.1.
When using facilities, projects, or police to suppress superdrones, a "ghost drone" would be formed, which would cancel talents and show up on the base screen, but would not show up on the psych breakdown or contribute to drone riots/prevent golden ages. This has been fixed as of version 2.1; now police suppress superdrones as they do drones, and facilities and projects can be set to either do the same (the default) or turn superdrones into drones before suppressing them (effectively suppressing one superdrone for the cost of two normal drones).
The bonus police unit granted by the Self-Aware Colony would be used instead of units with non-lethal methods, causing the project to actually make more drones in some cases. This has been fixed as of version 2.1.
The effects of nerve stapling and the punishment sphere were marked under "secret projects" in the psych breakdown; beginning with version 2.1, they do not appear at all in the psych breakdown, only on the base screen.
The Ascent to Transcendence could be built by the Caretakers, and would appear as a build option even if it had already been built; these have been fixed as of version 2.1.
When drone revolts affected a base, the faction gaining the base would be calculated incorrectly; this has been fixed as of version 2.2.
In Kyrub's patch, changing production, even to the same item, would cause the mineral gain from that turn to be cancelled. This has been fixed as of version 2.4.
If a satellite (Sky hydroponics, Nessus mining, Orbital power, or Orbital defense pod) is finished with nothing left in the queue, the base will not switch to Stockpile Energy, but rather begin making another of the same satellite.
Stockpile Energy now works slightly differently in several ways: The amount of energy produced is rounded down (rather than up), but will only spend as many minerals as it needs to in order to produce the maximum amount of energy. If there is anything in the mineral stores at the start of the turn, it will be added to the production to calculate how much energy to produce from Stockpile; conversely, if Stockpile is produced after finishing another item (which requires the ability to build multiple items per turn), only the carried-over minerals will contribute to Stockpile. Events that prevent production will have the same effects on Stockpile: A starving base will produce no energy from Stockpile, and a rioting base will convert stored minerals but not produce any new ones. The base screen will display the expected amount produced by Stockpile next turn, and will attempt to project the effects of these events based on the current state of the base (stored nutrients and net nutrients for starvation, current drones, superdrones, and talents for drone riots.) When changing production, Stockpile Energy will accurately predict the average long-term energy gain per turn under current production, truncating at 3 decimal places (it previously would fail to include the effects of the Planetary Energy Grid).
Killing off a human player will no longer crash the game.
Ending the turn where an air unit in the air has movement left will no longer cause all other air units to regenerate all fuel and prevent the turn number from progressing.
Artillery will no longer "intercept" other artillery from the same faction, or one with a truce or better.
Altitude will not be used in artillery duels between sea units, or (once the capability for air artillery is added) when one participant is an air unit.
Capturing a base from, or by, a faction with a free facility ability will now work properly.

More bugs fixed, thanks to Dio

The editor will no longer use the rainfall label improperly.
Fixed a bug involving the UI for the "go to base" option.
Created a new window.

Bugs targeted but not yet fixed

The count of a unit design rolls over at 255; this will hopefully be fixed in a future version.
The units lost of a given design may sometimes display incorrectly; this will hopefully be fixed in a future version.

Unfortunate consequences

Starting in version 1.1, the maximum number of landmarks has been decreased to 56, and most old maps will not work with the patch. These are all fixed as of version 2.0.
In the course of patching, various bugs and crashes are occasionally introduced by accident; these are generally fixed in the patch after they are discovered.
In version 1.1, Nessus Mining Stations could increase ecological damage in bases that receive an Aerospace Complex from the Cloudbase Academy; this has been fixed in version 1.2.
While it is possible to change the speed formula for air units beginning in version 1.2, the unit cost will be calculated as though they use the standard +2 per reactor; this has been fixed as of version 2.2.
Starting in version 2.0, it is possible to use invalid values for various variables in the RULES section of alphax.txt, causing crashes or bugs. The acceptable values will be noted, but the program will no longer protect users from failure to follow these guidelines.
Starting in version 2.0, the locations of some alphax variables have been moved around; as a result, using an old alphax file with the patched .exe program will cause bugs and possibly crashes.