diff --git a/examples/Cooling/CoolingBox/run.sh b/examples/Cooling/CoolingBox/run.sh
index 9cf6208e7777ebf66d8b434a11ebb24ecfacd156..8a0d717e49324cdc49301fa0c551d5b7da198d5e 100755
--- a/examples/Cooling/CoolingBox/run.sh
+++ b/examples/Cooling/CoolingBox/run.sh
@@ -21,7 +21,7 @@ then
 fi
 
 # Run SWIFT
-../swift --cosmology --hydro --cooling --threads=4 -n 1000 coolingBox.yml
+../../swift --cosmology --hydro --cooling --threads=4 -n 1000 coolingBox.yml
 
 # Check energy conservation and cooling rate
 python energy_plot.py
diff --git a/examples/Cooling/CoolingHalo/run.sh b/examples/Cooling/CoolingHalo/run.sh
index c7c00fe81c960925fe490cd3d65fbc49d331f2d0..ca086fc93d5c4c34567c4405d7f3670972bbde9d 100755
--- a/examples/Cooling/CoolingHalo/run.sh
+++ b/examples/Cooling/CoolingHalo/run.sh
@@ -4,7 +4,7 @@
 echo "Generating initial conditions for the isothermal potential box example..."
 python makeIC.py 10000 
 
-../swift --external-gravity --hydro --cooling --threads=16 cooling_halo.yml 2>&1 | tee output.log
+../../swift --external-gravity --hydro --cooling --threads=16 cooling_halo.yml 2>&1 | tee output.log
 
 python radial_profile.py 2. 200 100
 
diff --git a/examples/Cooling/CoolingHaloWithSpin/run.sh b/examples/Cooling/CoolingHaloWithSpin/run.sh
index 90d0cc84e78858e8d163ff51e25375b03c6818e5..17ec5251a1071e36413ba926d14a179c1d6ed36b 100755
--- a/examples/Cooling/CoolingHaloWithSpin/run.sh
+++ b/examples/Cooling/CoolingHaloWithSpin/run.sh
@@ -5,7 +5,7 @@ echo "Generating initial conditions for the isothermal potential box example..."
 python makeIC.py 10000 
 
 # Run SWIFT with external potential, SPH and cooling
-../swift --external-gravity --hydro --cooling --threads=1 cooling_halo.yml 2>&1 | tee output.log
+../../swift --external-gravity --hydro --cooling --threads=1 cooling_halo.yml 2>&1 | tee output.log
 
 # python radial_profile.py 10
 
diff --git a/examples/Cosmology/ComovingSodShock_1D/run.sh b/examples/Cosmology/ComovingSodShock_1D/run.sh
index 0d1fc4f1be8699929b2cf3b2ea2c8813ebef9f10..2eae1729e007ac087654cb7b04d0701542cb4c75 100755
--- a/examples/Cosmology/ComovingSodShock_1D/run.sh
+++ b/examples/Cosmology/ComovingSodShock_1D/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift --cosmology --hydro --threads=1 sodShock.yml 2>&1 | tee output.log
+../../swift --cosmology --hydro --threads=1 sodShock.yml 2>&1 | tee output.log
 
 # Plot the result
 python plotSolution.py 1
diff --git a/examples/Cosmology/ComovingSodShock_2D/run.sh b/examples/Cosmology/ComovingSodShock_2D/run.sh
index bd6cc317d75a3bd415f074c9eaf48511ab693598..1723153e3eff1f7d49970ed4e3d5f69b39b67a1a 100755
--- a/examples/Cosmology/ComovingSodShock_2D/run.sh
+++ b/examples/Cosmology/ComovingSodShock_2D/run.sh
@@ -13,6 +13,6 @@ then
 fi
 
 # Run SWIFT
-../swift --cosmology --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
+../../swift --cosmology --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
 
 python plotSolution.py 1
diff --git a/examples/Cosmology/ComovingSodShock_3D/run.sh b/examples/Cosmology/ComovingSodShock_3D/run.sh
index 00e4f669fdb1347ab1b34cfa11821ca011b73120..b2ee90ecf8d7eabacc8b2b848b406a233953c9e6 100755
--- a/examples/Cosmology/ComovingSodShock_3D/run.sh
+++ b/examples/Cosmology/ComovingSodShock_3D/run.sh
@@ -13,6 +13,6 @@ then
 fi
 
 # Run SWIFT
-../swift --cosmology --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
+../../swift --cosmology --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
 
 python plotSolution.py 1
diff --git a/examples/Cosmology/ConstantCosmoVolume/run.sh b/examples/Cosmology/ConstantCosmoVolume/run.sh
index c7180b5232428a25c253e6f59726497c363eb1f4..4a30410e868aef58b1a9dac0a3225e5844c5873f 100755
--- a/examples/Cosmology/ConstantCosmoVolume/run.sh
+++ b/examples/Cosmology/ConstantCosmoVolume/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --cosmology --self-gravity --threads=8 constant_volume.yml 2>&1 | tee output.log
+../../swift --hydro --cosmology --self-gravity --threads=8 constant_volume.yml 2>&1 | tee output.log
 
 # Plot the result
 python plotSolution.py $i
diff --git a/examples/Cosmology/ZeldovichPancake_3D/run.sh b/examples/Cosmology/ZeldovichPancake_3D/run.sh
index 4153f2598f65af54b80b066cf97f76e64c06fce2..0be82b2f003143f3a783b2939a4ae932952d02c0 100755
--- a/examples/Cosmology/ZeldovichPancake_3D/run.sh
+++ b/examples/Cosmology/ZeldovichPancake_3D/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --cosmology --self-gravity --threads=8 zeldovichPancake.yml 2>&1 | tee output.log
+../../swift --hydro --cosmology --self-gravity --threads=8 zeldovichPancake.yml 2>&1 | tee output.log
 
 # Plot the result
 for i in {0..119}
diff --git a/examples/EAGLE_DMO_low_z/EAGLE_DMO_100/run.sh b/examples/EAGLE_DMO_low_z/EAGLE_DMO_100/run.sh
index 6a3b3a00d69c6f3ff78159290d3e41c7d534b8ae..be3cdd8e3cbc4cdbb0d8ab039bbbaa0f8e9ce2a1 100755
--- a/examples/EAGLE_DMO_low_z/EAGLE_DMO_100/run.sh
+++ b/examples/EAGLE_DMO_low_z/EAGLE_DMO_100/run.sh
@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift --cosmology --self-gravity --threads=16 eagle_100.yml 2>&1 | tee output.log
+../../swift --cosmology --self-gravity --threads=16 eagle_100.yml 2>&1 | tee output.log
 
diff --git a/examples/EAGLE_DMO_low_z/EAGLE_DMO_12/run.sh b/examples/EAGLE_DMO_low_z/EAGLE_DMO_12/run.sh
index f5e7e729470d632aab9a539f50d3bb922b7ae88f..669fa49823cd65ff336c60964e5e565e925c53c5 100755
--- a/examples/EAGLE_DMO_low_z/EAGLE_DMO_12/run.sh
+++ b/examples/EAGLE_DMO_low_z/EAGLE_DMO_12/run.sh
@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift --cosmology --self-gravity --threads=16 eagle_12.yml 2>&1 | tee output.log
+../../swift --cosmology --self-gravity --threads=16 eagle_12.yml 2>&1 | tee output.log
 
diff --git a/examples/EAGLE_DMO_low_z/EAGLE_DMO_25/run.sh b/examples/EAGLE_DMO_low_z/EAGLE_DMO_25/run.sh
index 6387472050b46d84932d27739b9490b727d4d31f..6d96edda655c7bf2d18ab8312417722f78bdb7e0 100755
--- a/examples/EAGLE_DMO_low_z/EAGLE_DMO_25/run.sh
+++ b/examples/EAGLE_DMO_low_z/EAGLE_DMO_25/run.sh
@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift --cosmology --self-gravity --threads=16 eagle_25.yml 2>&1 | tee output.log
+../../swift --cosmology --self-gravity --threads=16 eagle_25.yml 2>&1 | tee output.log
 
diff --git a/examples/EAGLE_DMO_low_z/EAGLE_DMO_50/run.sh b/examples/EAGLE_DMO_low_z/EAGLE_DMO_50/run.sh
index 486f7f33f7a2062563d63873e823c8623f10cf0d..8a08d0b0408c39f58a53aeff660123f6afc5777b 100755
--- a/examples/EAGLE_DMO_low_z/EAGLE_DMO_50/run.sh
+++ b/examples/EAGLE_DMO_low_z/EAGLE_DMO_50/run.sh
@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift --cosmology --self-gravity --threads=16 eagle_50.yml 2>&1 | tee output.log
+../../swift --cosmology --self-gravity --threads=16 eagle_50.yml 2>&1 | tee output.log
 
diff --git a/examples/EAGLE_low_z/EAGLE_100/run.sh b/examples/EAGLE_low_z/EAGLE_100/run.sh
index 12b6ff2a6e3486f45a9a66a4cca3346336160a3d..28571d4803cb8c26bf67d84870c10a2e7dcf534c 100755
--- a/examples/EAGLE_low_z/EAGLE_100/run.sh
+++ b/examples/EAGLE_low_z/EAGLE_100/run.sh
@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift --cosmology --hydro --self-gravity --stars --threads=16 eagle_100.yml 2>&1 | tee output.log
+../../swift --cosmology --hydro --self-gravity --stars --threads=16 eagle_100.yml 2>&1 | tee output.log
 
diff --git a/examples/EAGLE_low_z/EAGLE_12/run.sh b/examples/EAGLE_low_z/EAGLE_12/run.sh
index 90128c4f6c291a86f90e794d452641b08248fbdc..bceddf338ae797abcc32c24fb2642320d9091ba9 100755
--- a/examples/EAGLE_low_z/EAGLE_12/run.sh
+++ b/examples/EAGLE_low_z/EAGLE_12/run.sh
@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift --cosmology --hydro --self-gravity --stars --threads=16 eagle_12.yml 2>&1 | tee output.log
+../../swift --cosmology --hydro --self-gravity --stars --threads=16 eagle_12.yml 2>&1 | tee output.log
 
diff --git a/examples/EAGLE_low_z/EAGLE_25/run.sh b/examples/EAGLE_low_z/EAGLE_25/run.sh
index 5961cf01a3a011ee26f0b411e619dd7207d5db47..ea14dbde3293bb28f98de29eb035d53bc7caa1e6 100755
--- a/examples/EAGLE_low_z/EAGLE_25/run.sh
+++ b/examples/EAGLE_low_z/EAGLE_25/run.sh
@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift --cosmology --hydro --self-gravity --stars --threads=16 eagle_25.yml 2>&1 | tee output.log
+../../swift --cosmology --hydro --self-gravity --stars --threads=16 eagle_25.yml 2>&1 | tee output.log
 
diff --git a/examples/EAGLE_low_z/EAGLE_50/run.sh b/examples/EAGLE_low_z/EAGLE_50/run.sh
index a08e3125b1a8c1d65013ebd537f033abf6de5c3e..e2f2836900bacf612acb289154de973cda90eccb 100755
--- a/examples/EAGLE_low_z/EAGLE_50/run.sh
+++ b/examples/EAGLE_low_z/EAGLE_50/run.sh
@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift --cosmology --hydro --self-gravity --stars --threads=16 eagle_50.yml 2>&1 | tee output.log
+../../swift --cosmology --hydro --self-gravity --stars --threads=16 eagle_50.yml 2>&1 | tee output.log
 
diff --git a/examples/EAGLE_low_z/EAGLE_6/run.sh b/examples/EAGLE_low_z/EAGLE_6/run.sh
index 6df5902a057434ad1e7b5145b235655fa981e40e..47dbd952549137d8c2baab8c22361a227eb35ca9 100755
--- a/examples/EAGLE_low_z/EAGLE_6/run.sh
+++ b/examples/EAGLE_low_z/EAGLE_6/run.sh
@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift --cosmology --hydro --self-gravity --stars --threads=16 eagle_6.yml 2>&1 | tee output.log
+../../swift --cosmology --hydro --self-gravity --stars --threads=16 eagle_6.yml 2>&1 | tee output.log
 
diff --git a/examples/GEAR/AgoraDisk/run.sh b/examples/GEAR/AgoraDisk/run.sh
index 6bf9a98342b4b1977579761da79e06226c6ded40..5b85be7df875cee69b513e36a327b1469e35b60e 100755
--- a/examples/GEAR/AgoraDisk/run.sh
+++ b/examples/GEAR/AgoraDisk/run.sh
@@ -38,7 +38,7 @@ cp $sim.hdf5 agora_disk.hdf5
 python3 changeType.py agora_disk.hdf5
 
 # Run SWIFT
-#../swift $flag --hydro --self-gravity --threads=4 agora_disk.yml 2>&1 | tee output.log
+#../../swift $flag --hydro --self-gravity --threads=4 agora_disk.yml 2>&1 | tee output.log
 
 
 echo "Changing smoothing length to be Gadget compatible"
diff --git a/examples/GEAR/DwarfGalaxy/run.sh b/examples/GEAR/DwarfGalaxy/run.sh
index 17c0ac0c7e3456c3b43ade953ed94052edb37ac8..1f63556e7f7af57885606c08fc8e1a923c2e440d 100755
--- a/examples/GEAR/DwarfGalaxy/run.sh
+++ b/examples/GEAR/DwarfGalaxy/run.sh
@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift --feedback --self-gravity --hydro --stars --threads=8 $@ dwarf_galaxy.yml 2>&1 | tee output.log
+../../swift --feedback --self-gravity --hydro --stars --threads=8 $@ dwarf_galaxy.yml 2>&1 | tee output.log
 
diff --git a/examples/GEAR/ZoomIn/run.sh b/examples/GEAR/ZoomIn/run.sh
index d9650dd7783ba90f732c222543c49d13256b4958..59c8ff0d63b504978e4d74abbce8680f65695ffa 100755
--- a/examples/GEAR/ZoomIn/run.sh
+++ b/examples/GEAR/ZoomIn/run.sh
@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift --feedback --cosmology --self-gravity --hydro --stars --threads=8 zoom_in.yml 2>&1 | tee output.log
+../../swift --feedback --cosmology --self-gravity --hydro --stars --threads=8 zoom_in.yml 2>&1 | tee output.log
 
diff --git a/examples/GiantImpacts/GiantImpact/run.sh b/examples/GiantImpacts/GiantImpact/run.sh
index 8c61d42f4e75d73595d387bed32eb7ce34a7d2a3..0324e72deed978b1095b15532e7c48eecc1a4276 100755
--- a/examples/GiantImpacts/GiantImpact/run.sh
+++ b/examples/GiantImpacts/GiantImpact/run.sh
@@ -17,7 +17,7 @@ fi
 cd ../GiantImpactUranus
 
 # Run SWIFT
-../swift -s -G -t 8 uranus_1e6.yml 2>&1 | tee output.log
+../../swift -s -G -t 8 uranus_1e6.yml 2>&1 | tee output.log
 
 # Plot the solution
 python3 plot_solution.py
diff --git a/examples/GravityTests/DiscPatch/GravityOnly/run.sh b/examples/GravityTests/DiscPatch/GravityOnly/run.sh
index 999ffa120f809ffe5aa0a3f104e53f8148cfe1c2..ab05b603254f62cdaebef49882407f441d006a2c 100755
--- a/examples/GravityTests/DiscPatch/GravityOnly/run.sh
+++ b/examples/GravityTests/DiscPatch/GravityOnly/run.sh
@@ -7,4 +7,4 @@ then
     python makeIC.py 1000
 fi
 
-../../swift --external-gravity --threads=2 disc-patch.yml
+../../../swift --external-gravity --threads=2 disc-patch.yml
diff --git a/examples/GravityTests/DiscPatch/HydroStatic/run.sh b/examples/GravityTests/DiscPatch/HydroStatic/run.sh
index 2dccc93f0445e03750bd090be073b7219b2cd353..44b933f79c1b0f699010932f285c62396de37a72 100755
--- a/examples/GravityTests/DiscPatch/HydroStatic/run.sh
+++ b/examples/GravityTests/DiscPatch/HydroStatic/run.sh
@@ -13,6 +13,6 @@ then
 fi
 
 # Run SWIFT
-../../swift --external-gravity --hydro --threads=4 disc-patch-icc.yml 2>&1 | tee output.log
+../../../swift --external-gravity --hydro --threads=4 disc-patch-icc.yml 2>&1 | tee output.log
 
 python plotSolution.py
diff --git a/examples/GravityTests/DiscPatch/HydroStatic_1D/run.sh b/examples/GravityTests/DiscPatch/HydroStatic_1D/run.sh
index 3e22727adab274a58110e43f127343b9bdcb0c82..a76db9422e12ee18251083ee8cf26dd28e861e69 100755
--- a/examples/GravityTests/DiscPatch/HydroStatic_1D/run.sh
+++ b/examples/GravityTests/DiscPatch/HydroStatic_1D/run.sh
@@ -8,6 +8,6 @@ then
 fi
 
 # Run SWIFT
-../../swift --external-gravity --hydro --threads=4 disc-patch-icc.yml 2>&1 | tee output.log
+../../../swift --external-gravity --hydro --threads=4 disc-patch-icc.yml 2>&1 | tee output.log
 
 python plotSolution.py
diff --git a/examples/GravityTests/ExternalPointMass/run.sh b/examples/GravityTests/ExternalPointMass/run.sh
index fa3a40e20c8101a3b5cdb5f0a443ac937cd680c7..6f96200e45ceabcece487005560c293cdc084780 100755
--- a/examples/GravityTests/ExternalPointMass/run.sh
+++ b/examples/GravityTests/ExternalPointMass/run.sh
@@ -8,6 +8,6 @@ then
 fi
 
 rm -rf pointMass_*.hdf5
-../swift --external-gravity --threads=1 externalPointMass.yml 2>&1 | tee output.log
+../../swift --external-gravity --threads=1 externalPointMass.yml 2>&1 | tee output.log
 
 python energy_plot.py
diff --git a/examples/GravityTests/Hernquist_circularorbit/run.sh b/examples/GravityTests/Hernquist_circularorbit/run.sh
index fe2eb0bd0780c3aa66d2b52b10e76b146fb9dde2..15cd929a5d2ba62efd4f7af378c9cad4788e7c5f 100755
--- a/examples/GravityTests/Hernquist_circularorbit/run.sh
+++ b/examples/GravityTests/Hernquist_circularorbit/run.sh
@@ -12,7 +12,7 @@ then
 fi
 
 # self gravity G, external potential g, hydro s, threads t and high verbosity v
-../swift --external-gravity --threads=6 hernquistcirc.yml 2>&1 | tee output.log
+../../swift --external-gravity --threads=6 hernquistcirc.yml 2>&1 | tee output.log
 
 
 echo "Save plots of the circular orbits"
diff --git a/examples/GravityTests/Hernquist_radialinfall/run.sh b/examples/GravityTests/Hernquist_radialinfall/run.sh
index 0ad64e2dd2c3c0bfd66f2da3d8bee1edb30fb5f2..7381f3ecd4f8aa6711d33607cec52d5cdfedccaf 100755
--- a/examples/GravityTests/Hernquist_radialinfall/run.sh
+++ b/examples/GravityTests/Hernquist_radialinfall/run.sh
@@ -12,7 +12,7 @@ then
 fi
 
 rm -rf hernquist_*.hdf5
-../swift --external-gravity --threads=1 hernquist.yml 2>&1 | tee output.log
+../../swift --external-gravity --threads=1 hernquist.yml 2>&1 | tee output.log
 
 
 
diff --git a/examples/GravityTests/HydrostaticHalo/run.sh b/examples/GravityTests/HydrostaticHalo/run.sh
index cb67be62aa014627c021ef784e68495cc48f637b..a3f8b04b1115e316736c1177ecfd8288ed2a045e 100755
--- a/examples/GravityTests/HydrostaticHalo/run.sh
+++ b/examples/GravityTests/HydrostaticHalo/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run for 10 dynamical times
-../swift --external-gravity --hydro --threads=1 hydrostatic.yml 2>&1 | tee output.log
+../../swift --external-gravity --hydro --threads=1 hydrostatic.yml 2>&1 | tee output.log
 
 echo "Plotting density profiles"
 mkdir plots
diff --git a/examples/GravityTests/IsothermalPotential/run.sh b/examples/GravityTests/IsothermalPotential/run.sh
index bc44b2bd1f05b84354f171801b9c2d6c28ea3641..4e6a502eddcc081549bc1c967cde9edab9f0b835 100755
--- a/examples/GravityTests/IsothermalPotential/run.sh
+++ b/examples/GravityTests/IsothermalPotential/run.sh
@@ -8,6 +8,6 @@ then
 fi
 
 rm -rf Isothermal_*.hdf5
-../swift --external-gravity --threads=1 isothermal.yml 2>&1 | tee output.log
+../../swift --external-gravity --threads=1 isothermal.yml 2>&1 | tee output.log
 
 python energy_plot.py
diff --git a/examples/GravityTests/NFW_Halo/run.sh b/examples/GravityTests/NFW_Halo/run.sh
index 3a21c9678487a070f568a67cccb989089e59d66a..7f16def75f760d2e4cef4a9303b7c370ebdd1916 100755
--- a/examples/GravityTests/NFW_Halo/run.sh
+++ b/examples/GravityTests/NFW_Halo/run.sh
@@ -11,7 +11,7 @@ then
 fi
 
 # self gravity G, external potential g, hydro s, threads t and high verbosity v
-../swift --external-gravity --threads=6 test.yml 2>&1 | tee output.log
+../../swift --external-gravity --threads=6 test.yml 2>&1 | tee output.log
 
 if command -v python3 &>/dev/null; then
     python3 makePlots.py
diff --git a/examples/HydroTests/EvrardCollapse_3D/run.sh b/examples/HydroTests/EvrardCollapse_3D/run.sh
index d9005a7214e297fc79053b5c2ca97b2cafc856a6..ae02bcc0baed1aff87c3866b77075f6cb0f89a27 100755
--- a/examples/HydroTests/EvrardCollapse_3D/run.sh
+++ b/examples/HydroTests/EvrardCollapse_3D/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --self-gravity --threads=4 evrard.yml 2>&1 | tee output.log
+../../swift --hydro --self-gravity --threads=4 evrard.yml 2>&1 | tee output.log
 
 # Get the high resolution 1D reference result if not present.
 if [ ! -e evrardCollapse3D_exact.txt ]
diff --git a/examples/HydroTests/Gradients/run.sh b/examples/HydroTests/Gradients/run.sh
index 4a0a80a3aef3a37c54108d1489abe80cb0fd3f10..86ee9a68389319b1cb5f7327e8bd689b6212e6c1 100755
--- a/examples/HydroTests/Gradients/run.sh
+++ b/examples/HydroTests/Gradients/run.sh
@@ -1,13 +1,13 @@
 #! /bin/bash
 
 python makeICs.py stretched
-../swift --hydro --threads=2 gradientsStretched.yml
+../../swift --hydro --threads=2 gradientsStretched.yml
 python plot.py gradients_stretched_0001.hdf5 stretched
 
 python makeICs.py cartesian
-../swift --hydro --threads=2 gradientsCartesian.yml
+../../swift --hydro --threads=2 gradientsCartesian.yml
 python plot.py gradients_cartesian_0001.hdf5 cartesian
 
 python makeICs.py random
-../swift --hydro --threads=2 gradientsRandom.yml
+../../swift --hydro --threads=2 gradientsRandom.yml
 python plot.py gradients_random_0001.hdf5 random
diff --git a/examples/HydroTests/GreshoVortex_2D/run.sh b/examples/HydroTests/GreshoVortex_2D/run.sh
index 855d528bdff2351cebb0602115f48a23bf4f1bc5..0e24112a0faafcd38a06216494f87888f3e132e2 100755
--- a/examples/HydroTests/GreshoVortex_2D/run.sh
+++ b/examples/HydroTests/GreshoVortex_2D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --threads=1 gresho.yml 2>&1 | tee output.log
+../../swift --hydro --threads=1 gresho.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 11
diff --git a/examples/HydroTests/GreshoVortex_3D/run.sh b/examples/HydroTests/GreshoVortex_3D/run.sh
index 1967a77ba70bfb30191df8fef6e1e5e7bd68e4eb..15b613782e685d86321460b33c52fe9109230840 100755
--- a/examples/HydroTests/GreshoVortex_3D/run.sh
+++ b/examples/HydroTests/GreshoVortex_3D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --threads=4 gresho.yml 2>&1 | tee output.log
+../../swift --hydro --threads=4 gresho.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 11
diff --git a/examples/HydroTests/InteractingBlastWaves_1D/run.sh b/examples/HydroTests/InteractingBlastWaves_1D/run.sh
index cb8519e7f924357c19271dfb8edd902f629a4649..42034d5e541c4e038a9284e88651cb6a9fa9013f 100755
--- a/examples/HydroTests/InteractingBlastWaves_1D/run.sh
+++ b/examples/HydroTests/InteractingBlastWaves_1D/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --threads=1 interactingBlastWaves.yml 2>&1 | tee output.log
+../../swift --hydro --threads=1 interactingBlastWaves.yml 2>&1 | tee output.log
 
 # Get the high resolution reference solution if not present.
 if [ ! -e interactingBlastWaves1D_exact.txt ]
diff --git a/examples/HydroTests/KelvinHelmholtzGrowthRate_2D/run.sh b/examples/HydroTests/KelvinHelmholtzGrowthRate_2D/run.sh
index 505d64498463bfa414ed30b25abb91ccd1b7f0df..4e565a2de588c53f54c928b3b9f7dfec483c8220 100755
--- a/examples/HydroTests/KelvinHelmholtzGrowthRate_2D/run.sh
+++ b/examples/HydroTests/KelvinHelmholtzGrowthRate_2D/run.sh
@@ -9,7 +9,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --threads=1 kelvinHelmholtzGrowthRate.yml 2>&1 | tee output.log
+../../swift --hydro --threads=1 kelvinHelmholtzGrowthRate.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 100
diff --git a/examples/HydroTests/KelvinHelmholtzGrowthRate_3D/run.sh b/examples/HydroTests/KelvinHelmholtzGrowthRate_3D/run.sh
index 505d64498463bfa414ed30b25abb91ccd1b7f0df..4e565a2de588c53f54c928b3b9f7dfec483c8220 100755
--- a/examples/HydroTests/KelvinHelmholtzGrowthRate_3D/run.sh
+++ b/examples/HydroTests/KelvinHelmholtzGrowthRate_3D/run.sh
@@ -9,7 +9,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --threads=1 kelvinHelmholtzGrowthRate.yml 2>&1 | tee output.log
+../../swift --hydro --threads=1 kelvinHelmholtzGrowthRate.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 100
diff --git a/examples/HydroTests/KelvinHelmholtz_2D/run.sh b/examples/HydroTests/KelvinHelmholtz_2D/run.sh
index ef823cb85b88ff1b228b6906835fac8383db8b8c..355bf052a7ad124bcb4d88254ad780a7ffa97aba 100755
--- a/examples/HydroTests/KelvinHelmholtz_2D/run.sh
+++ b/examples/HydroTests/KelvinHelmholtz_2D/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --threads=4 kelvinHelmholtz.yml 2>&1 | tee output.log
+../../swift --hydro --threads=4 kelvinHelmholtz.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 6
diff --git a/examples/HydroTests/KeplerianRing/run.sh b/examples/HydroTests/KeplerianRing/run.sh
index 236f512d1c9f5b5d660fc7d9f540c085ad3e29ab..b11a0c1e52f2792447ffe39efbdf5c7b2ddda437 100755
--- a/examples/HydroTests/KeplerianRing/run.sh
+++ b/examples/HydroTests/KeplerianRing/run.sh
@@ -9,7 +9,7 @@ then
 fi
 
 rm -rf keplerian_ring_*.hdf5
-../swift --external-gravity --hydro --threads=1 --verbose=1 keplerian_ring.yml 2>&1 | tee output.log
+../../swift --external-gravity --hydro --threads=1 --verbose=1 keplerian_ring.yml 2>&1 | tee output.log
 
 echo
 echo
diff --git a/examples/HydroTests/Noh_1D/run.sh b/examples/HydroTests/Noh_1D/run.sh
index 15efd56e7b5b41dedab31a8f1cbdf11e89a2704d..0a7bd0574c19428a7f82141e619aed1f49e677be 100755
--- a/examples/HydroTests/Noh_1D/run.sh
+++ b/examples/HydroTests/Noh_1D/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --threads=1 noh.yml 2>&1 | tee output.log
+../../swift --hydro --threads=1 noh.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 12
diff --git a/examples/HydroTests/Noh_2D/run.sh b/examples/HydroTests/Noh_2D/run.sh
index 5595ad8439eac02fd32dbb426e4affb41215d41a..36e2d7db554823c60bacbd2d907b9d06789a9fcd 100755
--- a/examples/HydroTests/Noh_2D/run.sh
+++ b/examples/HydroTests/Noh_2D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --threads=2 noh.yml 2>&1 | tee output.log
+../../swift --hydro --threads=2 noh.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 12
diff --git a/examples/HydroTests/Noh_3D/run.sh b/examples/HydroTests/Noh_3D/run.sh
index 7ff7b084f4b6297c76d3d60f4bde4ac7d12e944e..7845b5cfb592f0f8ac4c3951b48689623c06b21c 100755
--- a/examples/HydroTests/Noh_3D/run.sh
+++ b/examples/HydroTests/Noh_3D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --threads=2 noh.yml 2>&1 | tee output.log
+../../swift --hydro --threads=2 noh.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 12
diff --git a/examples/HydroTests/PerturbedBox_3D/run.sh b/examples/HydroTests/PerturbedBox_3D/run.sh
index ab771ea1f01e6cca3b9a3dc2cf02a4d596a64006..463f6fecf16e13c76d713bba3ef4112ffbde509c 100755
--- a/examples/HydroTests/PerturbedBox_3D/run.sh
+++ b/examples/HydroTests/PerturbedBox_3D/run.sh
@@ -7,4 +7,4 @@ then
     python makeIC.py 50
 fi
 
-../swift --hydro --threads=16 perturbedBox.yml 2>&1 | tee output.log
+../../swift --hydro --threads=16 perturbedBox.yml 2>&1 | tee output.log
diff --git a/examples/HydroTests/SedovBlast_1D/run.sh b/examples/HydroTests/SedovBlast_1D/run.sh
index e5674dc15e8fac1b36f43da07b829720c0ecd5f1..2888790eb1877541166c04002f9ae9539e9ef6d7 100755
--- a/examples/HydroTests/SedovBlast_1D/run.sh
+++ b/examples/HydroTests/SedovBlast_1D/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --limiter --threads=1 sedov.yml 2>&1 | tee output.log
+../../swift --hydro --limiter --threads=1 sedov.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 5
diff --git a/examples/HydroTests/SedovBlast_2D/run.sh b/examples/HydroTests/SedovBlast_2D/run.sh
index e2136f8f5e6ee9bde61d5189ed7955d53a3a9a6e..0ad75f9d378712bd62cdd47c66240976cc57f04c 100755
--- a/examples/HydroTests/SedovBlast_2D/run.sh
+++ b/examples/HydroTests/SedovBlast_2D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --limiter --threads=1 sedov.yml 2>&1 | tee output.log
+../../swift --hydro --limiter --threads=1 sedov.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 5
diff --git a/examples/HydroTests/SedovBlast_3D/run.sh b/examples/HydroTests/SedovBlast_3D/run.sh
index 7f0788cc822f1a6427fb6dbee4a921f79c942808..62af72bacca62cd18fa77300d887b0bf0dd20789 100755
--- a/examples/HydroTests/SedovBlast_3D/run.sh
+++ b/examples/HydroTests/SedovBlast_3D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --limiter --threads=4 sedov.yml 2>&1 | tee output.log
+../../swift --hydro --limiter --threads=4 sedov.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 5
diff --git a/examples/HydroTests/SineWavePotential_1D/run.sh b/examples/HydroTests/SineWavePotential_1D/run.sh
index a725a88a175ff39c20b958c07f2e7e84e388d417..920bd413a71a99e043cc7d31be088e0037c6c7c1 100755
--- a/examples/HydroTests/SineWavePotential_1D/run.sh
+++ b/examples/HydroTests/SineWavePotential_1D/run.sh
@@ -6,7 +6,7 @@ then
   python makeIC.py
 fi
 
-../swift --external-gravity --hydro --threads=2 sineWavePotential.yml 2>&1 | tee output.log
+../../swift --external-gravity --hydro --threads=2 sineWavePotential.yml 2>&1 | tee output.log
 
 for f in sineWavePotential_*.hdf5
 do
diff --git a/examples/HydroTests/SineWavePotential_2D/run.sh b/examples/HydroTests/SineWavePotential_2D/run.sh
index a725a88a175ff39c20b958c07f2e7e84e388d417..920bd413a71a99e043cc7d31be088e0037c6c7c1 100755
--- a/examples/HydroTests/SineWavePotential_2D/run.sh
+++ b/examples/HydroTests/SineWavePotential_2D/run.sh
@@ -6,7 +6,7 @@ then
   python makeIC.py
 fi
 
-../swift --external-gravity --hydro --threads=2 sineWavePotential.yml 2>&1 | tee output.log
+../../swift --external-gravity --hydro --threads=2 sineWavePotential.yml 2>&1 | tee output.log
 
 for f in sineWavePotential_*.hdf5
 do
diff --git a/examples/HydroTests/SineWavePotential_3D/run.sh b/examples/HydroTests/SineWavePotential_3D/run.sh
index a725a88a175ff39c20b958c07f2e7e84e388d417..920bd413a71a99e043cc7d31be088e0037c6c7c1 100755
--- a/examples/HydroTests/SineWavePotential_3D/run.sh
+++ b/examples/HydroTests/SineWavePotential_3D/run.sh
@@ -6,7 +6,7 @@ then
   python makeIC.py
 fi
 
-../swift --external-gravity --hydro --threads=2 sineWavePotential.yml 2>&1 | tee output.log
+../../swift --external-gravity --hydro --threads=2 sineWavePotential.yml 2>&1 | tee output.log
 
 for f in sineWavePotential_*.hdf5
 do
diff --git a/examples/HydroTests/SodShockSpherical_2D/run.sh b/examples/HydroTests/SodShockSpherical_2D/run.sh
index 90be0cc83c53bee0c53d3e522ce989d829549579..609f2e0ae065a1fa76ee7bcfa90efa9cb1aa020a 100755
--- a/examples/HydroTests/SodShockSpherical_2D/run.sh
+++ b/examples/HydroTests/SodShockSpherical_2D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --threads=1 sodShock.yml 2>&1 | tee output.log
+../../swift --hydro --threads=1 sodShock.yml 2>&1 | tee output.log
 
 # Get the high resolution 1D reference solution if not present.
 if [ ! -e sodShockSpherical2D_exact.txt ]
diff --git a/examples/HydroTests/SodShockSpherical_3D/run.sh b/examples/HydroTests/SodShockSpherical_3D/run.sh
index b28b69e0aa33d3a6657aae0db819298c66e26860..c511dbcc6b18248bcfd33a9e0216cd22cf26aead 100755
--- a/examples/HydroTests/SodShockSpherical_3D/run.sh
+++ b/examples/HydroTests/SodShockSpherical_3D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
+../../swift --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
 
 # Get the high resolution 1D reference solution if not present.
 if [ ! -e sodShockSpherical3D_exact.txt ]
diff --git a/examples/HydroTests/SodShock_1D/run.sh b/examples/HydroTests/SodShock_1D/run.sh
index fb2ba77daca880a36c58949983cf19fd631cb102..8be97f7b34c9947268ed44b44b2c445ddb8a717f 100755
--- a/examples/HydroTests/SodShock_1D/run.sh
+++ b/examples/HydroTests/SodShock_1D/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --threads=1 sodShock.yml 2>&1 | tee output.log
+../../swift --hydro --threads=1 sodShock.yml 2>&1 | tee output.log
 
 # Plot the result
 python plotSolution.py 1 
diff --git a/examples/HydroTests/SodShock_2D/run.sh b/examples/HydroTests/SodShock_2D/run.sh
index 730cabcb9d51c0c870b38512ad1ce6ed80253ebd..a11c6291a48447b2f64aef458c01036e4ed73441 100755
--- a/examples/HydroTests/SodShock_2D/run.sh
+++ b/examples/HydroTests/SodShock_2D/run.sh
@@ -13,6 +13,6 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --threads=1 sodShock.yml 2>&1 | tee output.log
+../../swift --hydro --threads=1 sodShock.yml 2>&1 | tee output.log
 
 python plotSolution.py 1
diff --git a/examples/HydroTests/SodShock_3D/run.sh b/examples/HydroTests/SodShock_3D/run.sh
index fee82ce3e1bbbe600fb170f6249f9063ab5aec70..aceeacd331e9d2e467e1cf42079dcb492ad0c631 100755
--- a/examples/HydroTests/SodShock_3D/run.sh
+++ b/examples/HydroTests/SodShock_3D/run.sh
@@ -13,6 +13,6 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
+../../swift --hydro --threads=4 sodShock.yml 2>&1 | tee output.log
 
 python plotSolution.py 1
diff --git a/examples/HydroTests/SquareTest_2D/run.sh b/examples/HydroTests/SquareTest_2D/run.sh
index f96bd4c0e19958f91c631616321a7280fa090c40..dae0d742e706d73f3a5efc26a9d82ac59c883757 100755
--- a/examples/HydroTests/SquareTest_2D/run.sh
+++ b/examples/HydroTests/SquareTest_2D/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --threads=1 square.yml 2>&1 | tee output.log
+../../swift --hydro --threads=1 square.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 5
diff --git a/examples/HydroTests/UniformBox_2D/run.sh b/examples/HydroTests/UniformBox_2D/run.sh
index 3c146d8b48d1e191b043a2ead52715cd49edf9e5..aad344187dfac468c58baa7b32e45024c8ef49b1 100755
--- a/examples/HydroTests/UniformBox_2D/run.sh
+++ b/examples/HydroTests/UniformBox_2D/run.sh
@@ -7,4 +7,4 @@ then
     python makeIC.py 100
 fi
 
-../swift --hydro --threads=16 uniformPlane.yml 2>&1 | tee output.log
+../../swift --hydro --threads=16 uniformPlane.yml 2>&1 | tee output.log
diff --git a/examples/HydroTests/UniformBox_3D/run.sh b/examples/HydroTests/UniformBox_3D/run.sh
index eb2648cc5277f830436dadf5902df5531985a3f0..f93c53a14c5441a7df8936f3507ce9cbe8c2294c 100755
--- a/examples/HydroTests/UniformBox_3D/run.sh
+++ b/examples/HydroTests/UniformBox_3D/run.sh
@@ -7,4 +7,4 @@ then
     python makeIC.py 100
 fi
 
-../swift --hydro --threads=16 uniformBox.yml 2>&1 | tee output.log
+../../swift --hydro --threads=16 uniformBox.yml 2>&1 | tee output.log
diff --git a/examples/HydroTests/VacuumSpherical_2D/run.sh b/examples/HydroTests/VacuumSpherical_2D/run.sh
index c88095abf3a94d4f9e9c007722896a8ac2303bb4..54c5efdf9623cd11e504753514052f05ad1b36eb 100755
--- a/examples/HydroTests/VacuumSpherical_2D/run.sh
+++ b/examples/HydroTests/VacuumSpherical_2D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --threads=4 vacuum.yml 2>&1 | tee output.log
+../../swift --hydro --threads=4 vacuum.yml 2>&1 | tee output.log
 
 # Get the 1D high resolution reference result if not present.
 if [ ! -e vacuumSpherical2D_exact.txt ]
diff --git a/examples/HydroTests/VacuumSpherical_3D/run.sh b/examples/HydroTests/VacuumSpherical_3D/run.sh
index ef6a84be13b3f4612b2d79237e9caa47fa0bd665..32a55a7478cbb70d8042154b19964269f337488c 100755
--- a/examples/HydroTests/VacuumSpherical_3D/run.sh
+++ b/examples/HydroTests/VacuumSpherical_3D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --threads=16 vacuum.yml 2>&1 | tee output.log
+../../swift --hydro --threads=16 vacuum.yml 2>&1 | tee output.log
 
 # Get the reference solution if it is not present.
 if [ ! -e vacuumSpherical3D_exact.txt ]
diff --git a/examples/HydroTests/Vacuum_1D/run.sh b/examples/HydroTests/Vacuum_1D/run.sh
index a840f7c1ba6ef4b938b53839f057072f1867a8b6..c5f7e0344e7a6517dae51390e2eae4acd80a5f5f 100755
--- a/examples/HydroTests/Vacuum_1D/run.sh
+++ b/examples/HydroTests/Vacuum_1D/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --threads=1 vacuum.yml 2>&1 | tee output.log
+../../swift --hydro --threads=1 vacuum.yml 2>&1 | tee output.log
 
 # Plot the result
 python plotSolution.py 1
diff --git a/examples/HydroTests/Vacuum_2D/run.sh b/examples/HydroTests/Vacuum_2D/run.sh
index 5a526bb5062fd6e5bf1dbe442689e915d4f20352..08f3ba19d69865112db6ac68f0264e19b6b4363b 100755
--- a/examples/HydroTests/Vacuum_2D/run.sh
+++ b/examples/HydroTests/Vacuum_2D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --threads=4 vacuum.yml 2>&1 | tee output.log
+../../swift --hydro --threads=4 vacuum.yml 2>&1 | tee output.log
 
 # Plot the result
 python plotSolution.py 1
diff --git a/examples/HydroTests/Vacuum_3D/run.sh b/examples/HydroTests/Vacuum_3D/run.sh
index eaf7a32d4f833af43cdea74829b768b53fb2f5e3..b75803f97fdd60a78efe9b05267e265d51fb1f1f 100755
--- a/examples/HydroTests/Vacuum_3D/run.sh
+++ b/examples/HydroTests/Vacuum_3D/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift --hydro --threads=16 vacuum.yml 2>&1 | tee output.log
+../../swift --hydro --threads=16 vacuum.yml 2>&1 | tee output.log
 
 # Plot the result
 python plotSolution.py 1
diff --git a/examples/IsolatedGalaxy/IsolatedGalaxy_dmparticles/run.sh b/examples/IsolatedGalaxy/IsolatedGalaxy_dmparticles/run.sh
index 5a4d5b6ce44150983fda6daf62cf0c77854e1845..604c01d09a3553c598bb5691e0078ae52592670d 100755
--- a/examples/IsolatedGalaxy/IsolatedGalaxy_dmparticles/run.sh
+++ b/examples/IsolatedGalaxy/IsolatedGalaxy_dmparticles/run.sh
@@ -6,7 +6,7 @@ then
     ./getIC.sh
 fi 
 
-../swift --external-gravity --self-gravity --stars --threads=16 isolated_galaxy.yml 2>&1 | tee output.log
+../../swift --external-gravity --self-gravity --stars --threads=16 isolated_galaxy.yml 2>&1 | tee output.log
 
 
 echo "Make plots of conservation of total angular momentum" 
diff --git a/examples/IsolatedGalaxy/IsolatedGalaxy_potential/run.sh b/examples/IsolatedGalaxy/IsolatedGalaxy_potential/run.sh
index e93b43b55bdb233282da05fb5098347969279f13..8c0f2011d4a2b633d69ab454d0309b98a05b7f24 100755
--- a/examples/IsolatedGalaxy/IsolatedGalaxy_potential/run.sh
+++ b/examples/IsolatedGalaxy/IsolatedGalaxy_potential/run.sh
@@ -6,7 +6,7 @@ then
     ./getIC.sh
 fi 
 
-../swift --external-gravity --self-gravity --stars --threads=16 isolated_galaxy.yml 2>&1 | tee output.log
+../../swift --external-gravity --self-gravity --stars --threads=16 isolated_galaxy.yml 2>&1 | tee output.log
 
 
 echo "Make plots of conservation of total angular momentum" 
diff --git a/examples/IsolatedGalaxy/IsolatedGalaxy_starformation/run.sh b/examples/IsolatedGalaxy/IsolatedGalaxy_starformation/run.sh
index 0b6aa8ea3b37ccb7e05fd33cbf414355b136db78..f2aa93fd0e11cd9b07be991187cf0780a82ebec8 100755
--- a/examples/IsolatedGalaxy/IsolatedGalaxy_starformation/run.sh
+++ b/examples/IsolatedGalaxy/IsolatedGalaxy_starformation/run.sh
@@ -6,7 +6,7 @@ then
     ./getIC.sh
 fi
 
-../swift --threads=32 --external-gravity --self-gravity --stars --star-formation --cooling --temperature --hydro isolated_galaxy.yml 2>&1 | tee output.log
+../../swift --threads=32 --external-gravity --self-gravity --stars --star-formation --cooling --temperature --hydro isolated_galaxy.yml 2>&1 | tee output.log
 
 # Kennicutt-Schmidt law plot
 python3 plotSolution.py
diff --git a/examples/SantaBarbara/SantaBarbara-128/run.sh b/examples/SantaBarbara/SantaBarbara-128/run.sh
index 206ba7bad03e0fff12e683ee10bbe2434a73a500..72c219acb201b3a3541b6a08d799b21ba4638009 100755
--- a/examples/SantaBarbara/SantaBarbara-128/run.sh
+++ b/examples/SantaBarbara/SantaBarbara-128/run.sh
@@ -1,4 +1,4 @@
 #!/bin/bash
 # Run SWIFT
-../swift --cosmology --hydro --self-gravity --threads=28 santa_barbara.yml
+../../swift --cosmology --hydro --self-gravity --threads=28 santa_barbara.yml
 
diff --git a/examples/SantaBarbara/SantaBarbara-256/run.sh b/examples/SantaBarbara/SantaBarbara-256/run.sh
index 206ba7bad03e0fff12e683ee10bbe2434a73a500..72c219acb201b3a3541b6a08d799b21ba4638009 100755
--- a/examples/SantaBarbara/SantaBarbara-256/run.sh
+++ b/examples/SantaBarbara/SantaBarbara-256/run.sh
@@ -1,4 +1,4 @@
 #!/bin/bash
 # Run SWIFT
-../swift --cosmology --hydro --self-gravity --threads=28 santa_barbara.yml
+../../swift --cosmology --hydro --self-gravity --threads=28 santa_barbara.yml
 
diff --git a/examples/SmallCosmoVolume/SmallCosmoVolume_DM/run.sh b/examples/SmallCosmoVolume/SmallCosmoVolume_DM/run.sh
index 9c002f4643ad3cad073e6c4a39066bc20cf7b52a..5d166e00a630ca93ff92a42f6d26b012b132e097 100755
--- a/examples/SmallCosmoVolume/SmallCosmoVolume_DM/run.sh
+++ b/examples/SmallCosmoVolume/SmallCosmoVolume_DM/run.sh
@@ -8,5 +8,5 @@ then
 fi
 
 # Run SWIFT
-../swift --cosmology --self-gravity --threads=8 small_cosmo_volume_dm.yml 2>&1 | tee output.log
+../../swift --cosmology --self-gravity --threads=8 small_cosmo_volume_dm.yml 2>&1 | tee output.log
 
diff --git a/examples/SmallCosmoVolume/SmallCosmoVolume_VELOCIraptor/run.sh b/examples/SmallCosmoVolume/SmallCosmoVolume_VELOCIraptor/run.sh
index cde550f0a52186b8284427606ff3b71aa718cd34..b89662ed7ae621c6fbc29ccfb566fa61367693a9 100755
--- a/examples/SmallCosmoVolume/SmallCosmoVolume_VELOCIraptor/run.sh
+++ b/examples/SmallCosmoVolume/SmallCosmoVolume_VELOCIraptor/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift --cosmology --hydro --self-gravity --velociraptor --threads=8 small_cosmo_volume.yml 2>&1 | tee output.log
+../../swift --cosmology --hydro --self-gravity --velociraptor --threads=8 small_cosmo_volume.yml 2>&1 | tee output.log
 
 echo "Make a plot of the HMF"
 if command -v python3 &>/dev/null; then
diff --git a/examples/SmallCosmoVolume/SmallCosmoVolume_cooling/run.sh b/examples/SmallCosmoVolume/SmallCosmoVolume_cooling/run.sh
index 5a2c67c77e2e2ec99d0c9659f6efac8434a818ed..5ce9e2bb3b544eb915f189d4aa417fcc9c316b64 100755
--- a/examples/SmallCosmoVolume/SmallCosmoVolume_cooling/run.sh
+++ b/examples/SmallCosmoVolume/SmallCosmoVolume_cooling/run.sh
@@ -14,7 +14,7 @@ then
 fi
 
 # Run SWIFT
-../swift --cosmology --hydro --self-gravity --cooling --threads=8 small_cosmo_volume.yml 2>&1 | tee output.log
+../../swift --cosmology --hydro --self-gravity --cooling --threads=8 small_cosmo_volume.yml 2>&1 | tee output.log
 
 # Plot the temperature evolution
 python plotTempEvolution.py
diff --git a/examples/SmallCosmoVolume/SmallCosmoVolume_hydro/run.sh b/examples/SmallCosmoVolume/SmallCosmoVolume_hydro/run.sh
index 12c98d1b636ef4ce324f861f6db236738785f856..b2585d70b7cd2b717af02f005d690d0e8a9f932e 100755
--- a/examples/SmallCosmoVolume/SmallCosmoVolume_hydro/run.sh
+++ b/examples/SmallCosmoVolume/SmallCosmoVolume_hydro/run.sh
@@ -8,7 +8,7 @@ then
 fi
 
 # Run SWIFT
-../swift --cosmology --hydro --self-gravity --threads=8 small_cosmo_volume.yml 2>&1 | tee output.log
+../../swift --cosmology --hydro --self-gravity --threads=8 small_cosmo_volume.yml 2>&1 | tee output.log
 
 # Plot the temperature evolution
 python plotTempEvolution.py
diff --git a/examples/SubgridTests/SmoothedMetallicity/run.sh b/examples/SubgridTests/SmoothedMetallicity/run.sh
index 9f31eac3692be4ce4ad6bb554d6a95c11d21e791..736a16fc14ece7b09e13b61cd8e04f9735e6cfc6 100755
--- a/examples/SubgridTests/SmoothedMetallicity/run.sh
+++ b/examples/SubgridTests/SmoothedMetallicity/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift --steps=1 --hydro --threads=4 smoothed_metallicity.yml 2>&1 | tee output.log
+../../swift --steps=1 --hydro --threads=4 smoothed_metallicity.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 1
diff --git a/examples/SubgridTests/SupernovaeFeedback/run.sh b/examples/SubgridTests/SupernovaeFeedback/run.sh
index 984cee2b415f2273f951ec997f4c81d65f1a4d4a..af8802164c528fe14b3d525827107868a8ac5720 100644
--- a/examples/SubgridTests/SupernovaeFeedback/run.sh
+++ b/examples/SubgridTests/SupernovaeFeedback/run.sh
@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift --external-gravity --feedback --hydro --stars --threads=4 SN_feedback.yml 2>&1 | tee output.log
+../../swift --external-gravity --feedback --hydro --stars --threads=4 SN_feedback.yml 2>&1 | tee output.log
 
 # Plot the solution
 # TODO