To those who wanted to add "DisablePhaseJumping" to structures/ships as a toggle-able ability, here's how I did it if you're still interested:
First off, I didn't want to overwrite the original always-on jump inhibition ability, so I made a new ability.  I'll name each file that needs created, post what I have in it, and then I'll name the files I changed and what I changed to support/use the new ability.... I'm using entrenchment btw, so my capships/frigates/structures etc have 5 abilities (0-4) instead of 4. This makes it much easier to add it to cap ships as they now have a free spot! 
K files created in order of use by the game:
AbilityHyperspaceDisable.entity:
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
researchPrerequisites
 NumResearchPrerequisites 0
nameStringID "IDS_ABILITY_HYPERSPACEDISABLE_NAME"
descStringID "IDS_ABILITY_HYPERSPACEDISABLE_DESCRIPTION"
hudIcon "HUDICON_ABILITY_BOOSTRESOURCEEXTRACTION"
smallHudIcon "HUDICON_ABILITY_BOOSTRESOURCEEXTRACTION_ACTIVE"
infoCardIcon ""
I used the Hudicons I did because I figured this out using the Psi tradeport toggleable ability "boost resource extraction".  If you want to change those to other hudicons or customs, you probably can... I'm happy with these images though 
 
BuffHyperspaceDisableSpawner.entity
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"
 
BuffHyperspaceDisableTarget.entity
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"
 
Then open "English.str", add 4 to the line "NumStrings" and add these 4 entries:
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."
The above steps all get the ability recognized/usable by the game, the following is an example of how to use it in-game:
Open a capship file (for example I'll use the Advent Radiance Battleship... "CAPITALSHIP_PSIBATTLESHIP.entity")
move that capital ship's passive ability to "ability4" (which is ability 5) (If a capital ship does not have any passive abilities, you'll have to choose one to remove, because any ability that's in spot 5 is not clickable on the main hud (just the point allocation hud).
Once the passive is in spot 5 (it's ok that you can't click it anywhere other than point allocation, because once it's Purchased, it's "always on"), add "AbilityHyperspaceDisable" to the spot where the passive ability was
That's it. Load the game, enable the mod with these files in it, create the capital ship you've edited, and you now can turn the ability to phase jump on/off for any enemy ships in range 
You can add this ability to any structure or ship with an ability list, just make sure that whichever spot you add it to has a space in-game for the button... Otherwise you can't click it! (starbases and capital ships only have 4 "windows" because of the upgrade button and point allocation button that each has respectively. Frigates have all 5 windows open for their 5 abilities) Again, passives in spot 5 still work because... they're passive! 