Refactor `convert_input` to Perform tasks via helper function

[Sweetdevil144]

Description

Following changes were performed :

• [x] Shift functions to check for missing files
• [x] Return from convert_input via a helper function
• [x] Refactor extra variables in run.meta.analysis
• [x] Update corresponding test files and add tests to ensure do_conversions isn't affected by current applied changes

Motivation and Context

The main motive for these changes is to simplify convert_input by trying to break some of its components and branch it to other functions.

This PR may fix a task within #3307

Review Time Estimate

• [ ] Immediately
• [x] Within one week
• [ ] When possible

Types of changes

• [ ] Bug fix (non-breaking change which fixes an issue)
• [x] New feature (non-breaking change which adds functionality)
• [ ] Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• [ ] My change requires a change to the documentation.
• [ ] My name is in the list of CITATION.cff
• [x] I have updated the CHANGELOG.md.
• [ ] I have updated the documentation accordingly.
• [x] I have read the CONTRIBUTING document.
• [x] I have added tests to cover my changes.
• [x] All new and existing tests passed.

[Sweetdevil144]

Why do docker stacks fail with following msg?

Dockerfile:29
--------------------
  28 |     WORKDIR /src
  29 | >>> RUN git -c http.sslVerify=false clone https://github.com/EDmodel/ED2.git \
  30 | >>>     && cd ED2/ED/build \
  31 | >>>     && curl -o make/include.mk.VM http://isda.ncsa.illinois.edu/~kooper/EBI/include.mk.opt.`uname -s` \
  32 | >>>     && if [ "${MODEL_VERSION}" != "git" ]; then git checkout "v.${MODEL_VERSION}"; fi \
  33 | >>>     && ./install.sh -g -p VM \
  34 | >>>     && mv /src/ED2/ED/build/ed_${BINARY_VERSION}-opt /src/ED2/ED/build/ed 
  35 |     
--------------------
ERROR: failed to solve: process "/bin/sh -c git -c http.sslVerify=false clone https://github.com/EDmodel/ED2.git     && cd ED2/ED/build     && curl -o make/include.mk.VM http://isda.ncsa.illinois.edu/~kooper/EBI/include.mk.opt.`uname -s`     && if [ \"${MODEL_VERSION}\" != \"git\" ]; then git checkout \"v.${MODEL_VERSION}\"; fi     && ./install.sh -g -p VM     && mv /src/ED2/ED/build/ed_${BINARY_VERSION}-opt /src/ED2/ED/build/ed" did not complete successfully: exit code: 1