More link fixes in md files

.gitignore

@@ -26,3 +26,4 @@
 *.Rhistory
 *venv*
 *.DS_Store
+/site

docs/CodeFlow.md

@@ -8,7 +8,7 @@
     The `-scenarios` argument points to the scenarios input file.
     These two files are linked with an index column called `selection`, representing the row from each file to use. [`FASTSim Vehicles`](https://github.nrel.gov/MBAP/fastsim/blob/eacc527fff54223e5e4ee1a624959ddebbf315b8/python/fastsim/vehicle.py#L145) and [`Scenarios`](https://github.com/NREL/T3CO-private/blob/9c0b19327fb60672185f087bea195a059e919cf2/t3co/run_scenario.py#L113) are the core data structures in **T3CO**
     
-     Example of [Scenario inputs](./ScenarioFile.md).
+     Example of [Scenario inputs](./models/ScenarioFile.md).
      
      Example of [FASTSim vehicle inputs](https://github.nrel.gov/MBAP/fastsim/blob/eacc527fff54223e5e4ee1a624959ddebbf315b8/python/fastsim/resources/FASTSim_py_veh_db.csv).
      
@@ -19,7 +19,7 @@
   - `if optimizing`
     - `run_moo(selection int, scenarios DataFrame, *args, **kwargs)` [link](https://github.com/NREL/T3CO-private/blob/731d07d9b2b25f6faff583348467fb79c0d5ccf6/run_scripts/sweep.py#L187)
     - get [get knobs-bounds & curves](https://github.com/NREL/T3CO-private/blob/4a91dc12add268faaa08a092ef6c8f010cb99f86/run_scripts/sweep.py#L88)
-      - note: optimization parameters (knobs) are implicitly activated by their minimum and maximum bounds being populated. See [Scenario inputs](./ScenarioFile.md). For example, if the row for your selection has populated values in columns `knob_min_ess_kwh` and `knob_max_ess_kwh` then that tells the optimizer that battery size, `ess_kwh`, is an optimization parameter (knob). The curves work the same way, for example `eng_eff_imp_curve_sel` being populated means that the opimization parameter for engine efficiency should be used.
+      - note: optimization parameters (knobs) are implicitly activated by their minimum and maximum bounds being populated. See [Scenario inputs](./models/ScenarioFile.md). For example, if the row for your selection has populated values in columns `knob_min_ess_kwh` and `knob_max_ess_kwh` then that tells the optimizer that battery size, `ess_kwh`, is an optimization parameter (knob). The curves work the same way, for example `eng_eff_imp_curve_sel` being populated means that the opimization parameter for engine efficiency should be used.
     - get [objectives and constraints](https://github.com/NREL/T3CO-private/blob/4a91dc12add268faaa08a092ef6c8f010cb99f86/run_scripts/sweep.py#L170)
       - note: unlike knobs, constraints need to be explicitly turned on with `True`. For example: The Scenario file will have `constraint_range` value of `True`, and by necessity the target range must be specified as well, in `target_range_mi` 
     - begin optimization [loop](https://github.com/NREL/T3CO-private/blob/731d07d9b2b25f6faff583348467fb79c0d5ccf6/t3co/moopack/moo.py#L361)

docs/models/PHEVs.md

@@ -6,11 +6,11 @@ Given that PHEVs follow along the same TCO and optimizaton path as other powertr
 
 - [Plug-in Hybrid Electric Vehicle Considerations](#plug-in-hybrid-electric-vehicle-considerations)
 	- [Contents](#contents)
-	- [PHEV Fuel Economy CD/CS ](#phev-fuel-economy-cdcs-)
-	- [PHEV Fuel Costs and Utility Factor ](#phev-fuel-costs-and-utility-factor-)
-	- [PHEV Acceleration \& Grade Tests ](#phev-acceleration--grade-tests-)
-	- [PHEV Optimization ](#phev-optimization-)
-	- [PHEV Special Inputs ](#phev-special-inputs-)
+	- [PHEV Fuel Economy CD/CS ](#phev-fuel-econ)
+	- [PHEV Fuel Costs and Utility Factor ](#phev-fuel-costs)
+	- [PHEV Acceleration \& Grade Tests ](#phev-accel-grade)
+	- [PHEV Optimization ](#phev-optimization)
+	- [PHEV Special Inputs ](#phev-special-inputs)
 	- [PHEVs Not Doing What You Want?](#phev-issues)
 
 ## PHEV Fuel Economy CD/CS <a name="phev-fuel-econ"></a>
@@ -99,11 +99,11 @@ It is worth noting that initial SOC inputs for grade and acceleration of PHEVs d
 	init soc:  0.85 max speed at 6% grade achvd 67.793
 	init soc:  0.95 max speed at 6% grade achvd 67.793
 
-## PHEV Optimization <a name="PHEVOptimization"></a>
+## PHEV Optimization <a name="phev-optimization"></a>
 
 PHEV optimization uses an optional, special input called `motor_power_override_kw_fc_demand_on_pct`. This is the percentage of motor power value set to the vehicle field `kw_fc_demand_on` to allow `kw_fc_demand_on` to increase or decrease proportionally with changes in `mc_max_kw` from the optimizer. This is described in more detail in the opimization docs.
 
-## PHEV Special Inputs <a name="special-inputs"></a>
+## PHEV Special Inputs <a name="phev-special-inputs"></a>
 
 |**PHEV** scenario file inputs| description | required/optional | default | range |
 |--|--|--|--|--|