remove local links in README that were broken for VitePress (#78)

* remove local links in README that were broken for VitePress

* remove more README links

homepage/README.md

@@ -3,7 +3,7 @@ This directory contains a nice VitePress homepage created roughly as described [
 
 ## Process to create manual content for this homepage
 
-Created the [../package.json](../package.json) file in the top level directory by copying the same file from `dms-vep-pipeline-3`.
+Created the `package.json` file in the top level directory by copying the same file from `dms-vep-pipeline-3`.
 
 Then loaded `nodejs` on the Hutch server using:
 
@@ -13,29 +13,30 @@ And then in the top-level repo directory ran:
 
     npm install
 
-To create [../package-lock.json](../package-lock.json).
+To create `package-lock.json1.
 
-Also updated the [../.gitignore](../.gitignore) to add the following lines:
+Also updated the top-level `.gitignore1 to add the following lines:
 
     node_modules/
     !homepage/.vitepress/
     homepage/.vitepress/cache/
     homepage/.vitepress/dist/
 
-Then copied the `homepage/.vitepress` subdirectory from `dms-vep-pipeline` to [.vitepress](.vitepress), and manually edited [.vitepress/config.mjs](.vitepress/config.mjs) to have the correct names for this repository.
+Then copied the `homepage/.vitepress` subdirectory from `dms-vep-pipeline` to `.vitepress` in this directory, and manually edited `.vitepress/config.mjs` to have the correct names for this repository.
 
-Then created [index.md](index.md) and the other Markdown files with the page content.
+Then created `index.md` and the other Markdown files with the page content.
 
-Also, placed manually generated images in [public/images/](public/images).
+Also, placed manually generated images in `./public/images/`.
 
 ## Process to add pipeline output for this homepage
-Added to the top-level repo configuration ([../config.yaml](../config.yaml)) the following two lines:
+Added to the top-level repo configuration (`config.yaml`)) the following two lines:
 
     homepage: homepage/public
     build_vitepress_homepage: true
 
-Essentially, these two lines copy the auto-generated documentation of the pipeline in [../docs/](../docs) to the [./public/](public) subdirectory here so they can be used in the docs.
-Then re-ran the pipeline which populated the [./public/](public) subdirectory with a copy of [../docs/](../docs).
+Essentially, these two lines copy the auto-generated documentation of the pipeline in `./docs`/
+to the `./public/` subdirectory here so they can be used in the docs.
+Then re-ran the pipeline which populated the `./public/` subdirectory.
 
 ## Visualizing the page
 To view the page, after making sure `nodejs` is loaded via:
@@ -49,6 +50,6 @@ then do (on the Hutch server):
 To make edits to the Markdown files and have them show up in the visualization, run above command from same terminal you are using to make edits, such as using `tmux` to make vertically split windows.
 
 ## Deploying the pipeline
-Set up the GitHub action to build the VitePress documentation by copying [../.github/workflows/deploy.yaml](../.github/workflows/deploy.yaml) from `dms-vep-pipeline-3` to this repo.
+Set up the GitHub action to build the VitePress documentation by copying `.github/workflows/deploy.yaml` from `dms-vep-pipeline-3` to this repo.
 
 Then set up the docs to render from the `gh-pages` branch of the repo.