docs(readme): remove usage from readme

Remove usage from README.md. That content will be in the docs only.

README.md

@@ -33,92 +33,6 @@ Sensitive environment variables are stored in the .env file. This file is includ
 - Create a `.env` file and copy into it the contents of `.env.template`
 - Get your [GitHub Access Token](https://help.github.com/articles/creating-a-personal-access-token-for-the-command-line/) and add to the `.env` file.
 
-### Usage
-
-RefChef comes with two main commands (`refchef-cook` and `refchef-menu`).
-When using either of the commands, you'll be prompted to create a `.refchef-config` file. Alternatively,
-you can create the config file in your home directory.
-
-Here's an example of `.refchef.config`
-```yaml
-config-yaml:
-  path-settings:
-    reference-directory: ~/data/references_dir # directory where references will be downloaded and processed.
-    github-directory: ~/data/git_local # local git repository where `master.yaml` is located.
-    remote-repository: user/repo # remote user and repository for version control of `master.yaml`
-  log-settings:
-    log: 'yes'
-  runtime-settings:
-    break-on-error: 'yes'
-    verbose: 'yes'
-```
-
-### `refchef-cook`:  
-This command will read a `master.yaml` located in the `github-directory` path from the config file. The `master.yaml` file contains a list of references, as well as metadata, and commands necessary to download them (see example below).  
-Arguments:  
-`--exectue, -e`: will execute all commands listed in the `master.yaml` for each reference, if reference doesn't exist in the location provided in the config file.  
-`--new, -n`: path to a new yaml file containing other references to be downloaded and appended to the `master.yaml`.  
-`--update, -u`: whether to update the remote git repository with the new `master.yaml`.
-
-Example run:  
-    1 - This will read in `new.yaml` file, append to `master.yaml` and update the remote GitHub repository.
-    `refchef-cook -e --new new.yaml --update`  
-
-    2 - This will process `master.yaml` only and won't update the remote GitHub repository:  
-    `refchef-cook -e`
-
-
-Example `master.yaml`
-```yaml
-reference_test1:
-  metadata:
-    name: reference_test1
-    species: mouse
-    organization: ucsc
-    downloader: aleith
-  levels:
-    references:
-      - component: primary
-        retrieve: true
-        commands:
-          - curl https://s3.us-east-2.amazonaws.com/refchef-tests/chr1.fa.gz
-          - md5 *.fa.gz > postdownload_checksums.md5
-          - gunzip *.gz
-          - md5 *.fa > final_checksums.md5
-reference_test2:
-  metadata:
-    name: reference_test2
-    species: human
-    organization: ucsc
-    downloader: fgelin
-  levels:
-    references:
-      - component: primary
-        retrieve: true
-        commands:
-          - curl https://s3.us-east-2.amazonaws.com/refchef-tests/chr1.fa.gz
-          - md5 *.fa.gz > postdownload_checksums.md5
-          - gunzip *.gz
-          - md5 *.fa > final_checksums.md5
-```
-
-
-### `refchef-menu`
-This command provides a way for the user to list all references present in the system, based on `master.yaml`, as well as filter the list of references based on metadata options.  
-Arguments:  
-`--filter`: used to filter references based on metadata. Takes a pair key:value, or a list of pairs separated by comma: `key:value,key2:value2,key3:value3...`
-
-Example:
-
-`refchef-menu`
-
-![menu](docs/assets/menu-full.png)
-
-`refchef-menu --filter species:human`
-
-![menu](docs/assets/menu-filtered.png)
-
-
 
 #### Contact
 Contact cbc-help@brown.edu - this is our general help line, so please specify that your issue is with this site's contents