Fix note and equations to md native + some links

...documentation/analysis/cost_estimation/getting-started.md

docs/documentation/analysis/cost_estimation/index.md

...ntation/analysis/cost_estimation/operating_cost_method.md

...nalysis/cost_estimation/run_your_first_cost_estimation.md

...umentation/analysis/ecological_assessment/aqi_schaefer.md

...ntation/analysis/ecological_assessment/getting-started.md

...umentation/analysis/ecological_assessment/lca_schaefer.md

...ation/analysis/ecological_assessment/mission_emissions.md

...on/analysis/weight_and_balance_analysis/basic-concepts.md

...cumentation/analysis/weight_and_balance_analysis/usage.md

docs/documentation/libraries/aircraftGeometry2/index.md

...mentation/libraries/aircraftGeometry2/tutorial-convert.md

...mentation/libraries/aircraftGeometry2/tutorial-factory.md

...entation/libraries/aircraftGeometry2/tutorial-geometry.md

docs/documentation/sizing/fuselage_design/design_method.md

docs/documentation/sizing/fuselage_design/getting-started.md

docs/documentation/sizing/fuselage_design/index.md

...mentation/sizing/fuselage_design/run_your_first_design.md

...mentation/sizing/fuselage_design/software_architecture.md

docs/documentation/sizing/initial_sizing/changelog.md