FSTrent (and anyone else interested), here are the steps necessary to make and implement the disable phase jump ability. (bear with me as this will be a LOT of text)
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First how to create the ability for use:
1.) Create a new text file called "AbilityHyperspaceDisable".entity and paste the following (make sure to leave 1 extra empty line at the end of the file (meaning after - infoCardIcon "" hit enter once)):
TXT
entityType "Ability"
buffInstantActionType "ApplyOrRemoveBuffToSelf"
instantActionTriggerType "AlwaysPerform"
buffType "BuffHyperspaceDisableSpawner"
effectInfo
effectAttachInfo
attachType "Invalid"
smallEffectName ""
largeEffectName ""
soundID ""
toggleStateOnNameStringID "IDS_ABILITY_HYPERSPACEDISABLEACTIVE_NAME"
toggleStateOnDescStringID "IDS_ABILITY_HYPERSPACEDISABLEACTIVE_DESCRIPTION"
needsToFaceTarget FALSE
canCollideWithTarget TRUE
moveThruTarget FALSE
isUltimateAbility FALSE
maxNumLevels 1
levelSourceType "FixedLevel0"
aiUseTime "Anytime"
aiUseTargetCondition "Any"
isAutoCastAvailable TRUE
isAutoCastOnByDefault FALSE
pickRandomPlanetToExploreForAutoCastTarget FALSE
ignoreNonCombatShipsForAutoCastTarget TRUE
onlyAutoCastWhenDamageTakenExceedsPerc 0.000000
useCostType "AntiMatter"
antiMatterCost
Level:0 0.000000
Level:1 0.000000
Level:2 0.000000
cooldownTime
Level:0 0.000000
Level:1 0.000000
Level:2 0.000000
orderAcknowledgementType "ONGENERALORDERISSUED"
researchPrerequisites
NumResearchPrerequisites 0
nameStringID "IDS_ABILITY_HYPERSPACEDISABLE_NAME"
descStringID "IDS_ABILITY_HYPERSPACEDISABLE_DESCRIPTION"
hudIcon "HUDICON_ABILITY_BOOSTRESOURCEEXTRACTION"
smallHudIcon "HUDICON_ABILITY_BOOSTRESOURCEEXTRACTION_ACTIVE"
infoCardIcon ""
2.) make a new text file named "BuffHyperspaceDisableSpawner".entity and paste the following (again adding the 1 extra empty line at the end of the file)
TXT
entityType "Buff"
onReapplyDuplicateType "PrioritizeOldBuffs"
buffStackingLimitType "ForAllPlayers"
stackingLimit 1
allowFirstSpawnerToStack FALSE
buffExclusivityForAIType "ExclusiveForAllPlayers"
isInterruptable FALSE
isChannelling FALSE
numInstantActions 0
numPeriodicActions 1
periodicAction
actionCountType "Infinite"
actionIntervalTime
Level:0 2.500000
Level:1 0.000000
Level:2 0.000000
buffInstantActionType "ApplyBuffToTargetsInRadius"
instantActionTriggerType "AlwaysPerform"
buffType "BuffHyperspaceDisableTarget"
targetFilter
numOwnerships 1
ownership "Enemy"
numObjects 2
object "CapitalShip"
object "Frigate"
numSpaces 1
space "Normal"
numConstraints 0
range
Level:0 50000.000000
Level:1 0.000000
Level:2 0.000000
maxTargetCount
Level:0 -1.000000
Level:1 -1.000000
Level:2 -1.000000
effectInfo
effectAttachInfo
attachType "Invalid"
smallEffectName ""
largeEffectName ""
soundID ""
numOverTimeActions 0
numEntityModifiers 0
numEntityBoolModifiers 0
numFinishConditions 1
finishCondition
finishConditionType "OwnerChanged"
3.) make 1 more new text file named "BuffHyperspaceDisableTarget".entity and paste the following (and 1 more time adding that extra empty line at the bottom again):
TXT
entityType "Buff"
onReapplyDuplicateType "PrioritizeOldBuffs"
buffStackingLimitType "ForAllPlayers"
stackingLimit -1
buffExclusivityForAIType "NotExclusive"
isInterruptable FALSE
isChannelling FALSE
numInstantActions 0
numPeriodicActions 0
numOverTimeActions 0
numEntityModifiers 0
numEntityBoolModifiers 1
entityBoolModifier "DisablePhaseJump"
numFinishConditions 3
finishCondition
finishConditionType "FirstSpawnerNoLongerHasBuff"
buffTypeToQuery "BuffHyperspaceDisableSpawner"
finishCondition
finishConditionType "OutOfRange"
finishCondition
finishConditionType "OwnerChanged"
4.) Add these 4 entries to the end of the file English.str (and increase the count at the top by 4 too, and as above leave an extra blank line at the end of the file):
StringInfo
ID "IDS_ABILITY_HYPERSPACEDISABLEACTIVE_NAME"
Value "Stop Phase Space Jamming."
StringInfo
ID "IDS_ABILITY_HYPERSPACEDISABLEACTIVE_DESCRIPTION"
Value "Ships are once again allowed to phase jump."
StringInfo
ID "IDS_ABILITY_HYPERSPACEDISABLE_NAME"
Value "Begin Phase Space Jamming."
StringInfo
ID "IDS_ABILITY_HYPERSPACEDISABLE_DESCRIPTION"
Value "Jams the Phase space engine on enemy ships preventing phase jumps."
5.) (if making this mod for entrenchment), add the above three names (including the .entity and in quotes) to the "entity.manifest" file (I added mine in alphabetical order when I first converted to entrenchment1.01, I'm not sure if that's necessary or not...it works though)
6.) Create a "MyMod" folder (or whatever you want to call it if you're not using someone elses mod) within the {ModPath} for your computer; create a subfolder called "GameInfo" within "MyMod" and put the 3 .entity files within; create a "String" subfolder within "MyMod" and put the "English.str" file in there; and finally put the entity.manifest file within the "MyMod" folder.
If you're adding this to someone elses mod, just add the new entity files to their GameInfo folder; do step 5 to their "entity.manifest" file; and add those 4 string entries to their "English.str" file (as well as add 4 to their count)
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OK those steps (well and selecting the mod ingame of course) just make the ability ready for use by... whatever can use abilities. The following steps show how to add the ability to various things and some tips for doing so.
1.) Think of something you want to add this ability to such as the Vasari's Phase Jump Inhibitor ("PLANETMODULE_PHASEORBITALJUMPBLOCKER.entity") and open it up (the txt version, not the binary one... if you don't have the txt version, convert the one from the sins install directory)
1a.) decide where you want the button to show up in-game (TOP row 1st square 2nd squar etc to 5th square), and place the following text within the quotes after that ability#-1 within the entity file of whatever you're adding the ability to without the parenthesis (AbilityHyperspaceDisable). Since that last sentence was a bit convoluted, here's an example using the Vasari's PLANETMODULE_PHASEORBITALJUMPBLOCKER.entity:
open the file: pretend you want this new button to be in the 3rd square (the phase disruption icon is in square 1 which is ability:0 ), so type/paste AbilityHyperspaceDisable within the quotes after "Ability:2". Save and close the file. Add this file as well to your little mod (only 4 files in GameInfo, the 1 changed "entity.manifest" file in "MyMod", and the changed "English.str" in the "String" folder), load up the game, load up the mod, start a new game as Vasari, create a Phase Jump Inhibitor, click the button once (to turn it on), and enjoy the stuck enemies! 
INFORMATION: Structures (both tactical and civilian) have their abilities listed at the top of their ".entity" files; Capital Ships and Starbases Ditto; Fighters abilities show up at the very bottom of their corresponding "squad__.entity" file, and Frigates abilities show up really close to the bottom of their ".entity" files.
If you want to be able to use this ability, it must be in an ability slot that is visible in game (for fighters/frigates/structures, this can be any of the five, as all five spots are unoccupied in-game...except for abilities of course) For starbases and Capital ships though you only have 4 visible spots (the fifth is for the upgrade button for starbases and the ability-management button for capital ships)... Don't worry though! this just means you need to move one of that items PASSIVE abilitlies into spot 5 and put the AbilityHyperspaceDisable in its old spot (abilities in spot 5 are still there, you just can't click them cuz of the other button overwriting them.... passives don't have to be clicked to work)
so because of the above paragraph, this is what I did myself:
all starbases have the passive "AbilityDestabilizeHyperspace" ability. move this to Ability:4 (which is 5), and put the new ability in its old spot
all 3 races have at least 2 capital ships with at least 1 passive ability. Move that passive to Ability:4(which is 5), and put the new ability in its old spot (if you absolutely must have this phase-stopping ability on a capital with no passives, you will have to either A.) replace one of its clickable abilities with this one, or B.) Make this ability passive and just put it in spot 5 (ability:4) I made it toggleable so I could turn it off to let them run away if I was attacking with a monstrously larger force.
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well that's it for that. In case you're interested, I also found out how to make it so when playing as a vasari, I can use phase stabalizers to go from a planet to that systems Star (if it has a starbase with the phase stabalizer upgrade): If interested, keep reading. If not, skip the rest of this post 
_________________BEGIN PHASE JUMP TO STAR EXPLANATION___________________
I altered 3 files. I'm pretty sure only 1 is needed, but I did all three at once (for various reasons), and since everything was working the way I wanted I didn't want to expirement. I'll list the steps in importance:
1.) I feel confident betting this is the only change needed for this to work: Open "BuffPhaseGateStarBaseSelf.entity"; look in the "instant action" section; look in the "target filter" section; the 5th and 6th lines down in this section say (numObjects 1) and (object "Planet") respectively. Just make the "1" a "2", and make a newline after "planet" that says (object "Star"); save and close the file... add it to your mod (in the GameInfo folder)
2.) If step 1 doesn't do the trick by itself, this step will more than likely finish it: Open "BuffPhaseGateModuleSpawnerCaster.entity", and repeat the steps from above
3.) If steps 1 and 2 don't work completely, this third step will finish it (as these are the only 3 things I changed): Open "AbilityPhaseGateStarBase.entity", and change it's useCostType from "antimatter" to "Passive". when you do that, you also need to delete the next 8 lines (these are the entry for 3 levels of antimattercost, and 3 levels of cooldowntime). You will also need to open "BuffPhaseGateStarBaseSelf.entity"; change the bottom variable "numFinishConditions" to 0, and delete the following 6 lines (1 = finishCondition,2 = finishConditionType "TimeElapsed", 3 = time,
4= Level:0 ??.000000
5= Level:1 ??.000000
6= Level:2 ??.000000 (the file should have 1 empty newline after "numFinishConditions 0", and then nothing else)
Save both files (abilityPhaseGateStarBase and buffPhaseGateStarBaseSelf) close them and add them to your mods GameInfo folder.
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Voila, now you can phase jump from a planet with a phase gate to that planet's star (if you have a starbase upgraded with phasegates there).... not sure if it works for the ship version too as I don't build those ships. If the above 3 steps don't make it work, you could probably make it a passive (always on) ability too!
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