More README updates

# CAID-tools

Depi is a suite of tools for tracking dependencies across different types of resources stored in different ways. At the core is the depi-server which provides a protocol over gRPC. For the supported tools there are user-interfaces implemented as vscode-extensions and adapter/monitors that report in updates to the stored resources. The currently supported tools are `git`, `git-gsn` and `webgme`.

- **depi-impl** contains the source code for the depi-server, git-monitor, git-gsn-monitor, depi-cli and the depi vscode extension

- **examples** contains example models and utility scripts for docker (both for docker compose and the monolithic container)

- **gsn-domain** contains the vscode extension together with LSP for the GSN Assurance grammar

- **webgme-depi** contains a vscode extension wrapping a webgme instance (and webgme components providing the interface between these two)

## Repository structure

- `depi-impl` contains the source code for the depi-server, git-monitor, git-gsn-monitor, depi-cli and the depi vscode extension

- `examples` contains example models and utility scripts for docker (both for docker compose and the monolithic container)

- `gsn-domain` contains the source code for vscode extension GSN Editor which contains a grammar, LSP-server and a graphical editor for modeling assurance cases

- `webgme-depi` contains a vscode extension wrapping a webgme instance (and webgme components providing the interface between these two)

## Getting started

### Back-end Services

Start the back-end services first.

```

docker run --rm --name caid -p 3000:3000 -p 8888:8888 -p 5150:5150 git.isis.vanderbilt.edu:5050/aa-caid/caid-tools/caid-tools:0.1.7

docker run --rm --name caid -p 3000:3000 -p 8888:8888 -p 5150:5150 git.isis.vanderbilt.edu:5050/aa-caid/caid-tools/caid-tools:latest

```

The following services are running within the monolithic caid-tools container (see `examples/docker-compose.yml` for a more realistic deployment setup with individual containers for the different services).

- **depi-server** is the main server that tracks resources across different tools. In the monolithic Docker container, it persists the state in JSON files, which does not necessarily scale well. For non-demo purposes, the depi-server also supports [Dolt DB](https://github.com/dolthub/dolt) as a persistent layer.

- **git-monitor** TODO:

- **git-gsn-monitor** TODO:

- **webgme-server** TODO:

- **webgme-monitor** TODO:

- **gitea** TODO:

### Front-end/User Interface

TODO: Brief intro about why we use vscode and GUIs

- [Depi Browser](depi-impl/vscode-depi/README.md)

- [WebGME Client](webgme-depi/vscode-webgme-depi/README.md)

- [GSN Editor](gsn-domain/gsn-vscode-xtext/vscode-extension-self-contained/README.md)

  - This extension requires java 8+

Then the theia IDE with the extensions.

```

docker run --rm --name caid-fe -p 4000:4000 --network="host" git.isis.vanderbilt.edu:5050/aa-caid/caid-tools/caid-front-end:0.1.7

docker run --rm --name caid-fe -p 4000:4000 --network="host" git.isis.vanderbilt.edu:5050/aa-caid/caid-tools/caid-front-end:latest

```

Once up and running go to: [http://localhost:4000](http://localhost:4000) using your browser (tested with Chrome).

Install the linked vscode-extensions by searching for their name in the extensions menu under market place in your vscode instance.

- Depi Manager

- WebGME Depi

- GSN Assurance

  - This extension requires java 8+ [for more details about this extenion click here.](https://github.com/vu-isis/gsn-domain/tree/main/gsn-vscode-xtext/vscode-extension-self-contained#gsn-assurance-vscode)

- Depi Browser

- WebGME Client

- GSN Editor

  - This extension requires java 8+ [for more details about this extenion click here.](../gsn-domain/gsn-vscode-xtext/vscode-extension-self-contained/README.md)

#### Settings

 - To edit the user settings JSON do `Ctrl/Cmd + Shift + P` and start typing `Open User Settings (JSON)`. Invoke the command and paste the following into the JSON file.

# git clone git@git.isis.vanderbilt.edu:aa-caid/caid-tools.git

# cd caid-tools

# git submodule update --init

# ./publish.sh 1.0.0

git submodule update --init

if [ -z "$1" ]; then

    echo "Error: Pass version number x.x.x as argument!"

    exit 1

rm ".gitmodules"

# Read the file containing the list of files to delete (make sure to end with line-break)

# Read the file containing the list of files to delete (make sure to end with a line-break in the black_list_files.txt)

while read -r file; do

    if [ -e "$file" ]; then

        echo "Deleting file: $file"