diff --git a/runatlantis.io/docs/server-configuration.md b/runatlantis.io/docs/server-configuration.md
index 7fb8e515e..092513265 100644
--- a/runatlantis.io/docs/server-configuration.md
+++ b/runatlantis.io/docs/server-configuration.md
@@ -6,9 +6,6 @@ Configuration to `atlantis server` can be specified via command line flags,
 
 [[toc]]
 
-## Flags
-To see which flags are available, run `atlantis server --help`.
-
 ## Environment Variables
 All flags can be specified as environment variables.
 
@@ -25,7 +22,7 @@ The flag `--atlantis-url` is set by the environment variable `ATLANTIS_ATLANTIS_
 ## Config File
 All flags can also be specified via a YAML config file.
 
-To use a YAML config file, run `atlantis serer --config /path/to/config.yaml`.
+To use a YAML config file, run `atlantis server --config /path/to/config.yaml`.
 
 The keys of your config file should be the same as the flag names, ex.
 ```yaml
@@ -45,42 +42,347 @@ Values are chosen in this order:
 1. Config File
 
 
-## Notes On Specific Flags
-### `--automerge`
-See [Automerging](automerging.html)
-
-### `--checkout-strategy`
-See [Checkout Strategy](checkout-strategy.html)
-
-### `--default-tf-version`
-See [Terraform Versions](terraform-versions.html)
-
-### `--repo-whitelist`
-Atlantis requires you to specify a whitelist of repositories it will accept webhooks from via the `--repo-whitelist` flag.
-
-Notes:
-* Accepts a comma separated list, ex. `definition1,definition2`
-* Format is `{hostname}/{owner}/{repo}`, ex. `github.com/runatlantis/atlantis`
-* `*` matches any characters, ex. `github.com/runatlantis/*` will match all repos in the runatlantis organization
-* For Bitbucket Server: `{hostname}` is the domain without scheme and port, `{owner}` is the name of the project (not the key), and `{repo}` is the repo name
-
-Examples:
-* Whitelist `myorg/repo1` and `myorg/repo2` on `github.com`
-  * `--repo-whitelist=github.com/myorg/repo1,github.com/myorg/repo2`
-* Whitelist all repos under `myorg` on `github.com`
-  * `--repo-whitelist='github.com/myorg/*'`
-* Whitelist all repos in my GitHub Enterprise installation
-  * `--repo-whitelist='github.yourcompany.com/*'`
-* Whitelist all repositories
-  * `--repo-whitelist='*'`
+## Flags
+* ### `--allow-fork-prs`
+  ```bash
+  atlantis server --allow-fork-prs
+  ```
+  Respond to pull requests from forks. Defaults to `false`.
   
-### `--silence-whitelist-errors`
-Some users use the `--repo-whitelist` flag to control which repos Atlantis
-responds to. Normally, if Atlantis receives a pull request webhook from a repo not listed
-in the whitelist, it will comment back with an error. This flag disables that commenting.
+  :::warning SECURITY WARNING
+  Potentially dangerous to enable
+  because if attackers can create a pull request to your repo then they can cause Atlantis
+  to run arbitrary code. This can happen because
+  Atlantis will automatically run `terraform plan`
+  which can run arbitrary code if given a malicious Terraform configuration.
+  :::
+  
+* ### `--allow-repo-config`
+  <Badge text="Deprecated" type="warn"/>
+  ```bash
+  atlantis server --allow-repo-config
+  ```
+  This flag is deprecated. It allows all repos to use all restricted
+  `atlantis.yaml` keys. See [Repo Level Atlantis.yaml](repo-level-atlantis-yaml.html) for more details.
+  
+  Instead of using this flag, create a server-side `--repo-config` file:
+  ```yaml
+  # repos.yaml
+  repos:
+  - id: /.*/
+    allowed_overrides: [apply_requirements, workflow]
+    allow_custom_workflows: true
+  ```
+  Or use
+  ```bash
+  --repo-config-json='{"repos":[{"id":"/.*/", "allowed_overrides":["apply_requirements","workflow"], "allow_custom_workflows":true}]}'
+  ````
+  
+  ::: warning SECURITY WARNING
+  This setting enables pull requests to run arbitrary code on the Atlantis server.
+  Only enable in trusted settings.
+  :::
 
-Some users find this useful because they prefer to add the Atlantis webhook
-at an organization level rather than on each repo.
+* ### `--atlantis-url`
+  ```bash
+  atlantis server --atlantis-url="https://my-domain.com:9090/basepath"
+  ```
+  Specify the URL that Atlantis is accessible from. Used in the Atlantis UI
+  and in links from pull request comments. Defaults to `http://$(hostname):$port`
+  where `$port` is from the [`--port`](#port) flag. Supports a basepath if you're hosting Atlantis under a path.
 
-### `--tfe-token`
-A token for Terraform Enterprise integration. See [Terraform Enterprise](terraform-enterprise.html) for more details.
+* ### `--automerge`
+  ```bash
+  atlantis server --automerge
+  ```
+  Automatically merge pull requests after all plans have been successfully applied.
+  Defaults to `false`. See [Automerging](automerging.html) for more details.
+
+* ### `--bitbucket-base-url`
+  ```bash
+  atlantis server --bitbucket-base-url="http://bitbucket.corp:7990/basepath"
+  ```
+  Base URL of Bitbucket Server (aka Stash) installation. Must include
+  `http://` or `https://`. If using Bitbucket Cloud (bitbucket.org), do not set. Defaults to
+  `https://api.bitbucket.org`.
+  
+* ### `--bitbucket-token`
+  ```bash
+  atlantis server --bitbucket-token="token"
+  # or (recommended)
+  ATLANTIS_BITBUCKET_TOKEN='token' atlantis server
+  ```
+  Bitbucket app password of API user.
+
+* ### `--bitbucket-user`
+  ```bash
+  atlantis server --bitbucket-user="myuser"
+  ```
+  Bitbucket username of API user.
+  
+* ### `--bitbucket-webhook-secret`
+  ```bash
+  atlantis server --bitbucket-webhook-secret="secret"
+  # or (recommended)
+  ATLANTIS_BITBUCKET_WEBHOOK_SECRET='secret' atlantis server
+  ```
+  Secret used to validate Bitbucket webhooks. Only Bitbucket Server supports webhook secrets.
+  For Bitbucket.org, see [Security](security.html#bitbucket-cloud-bitbucket-org) for mitigations.
+  
+  ::: warning SECURITY WARNING
+  If not specified, Atlantis won't be able to validate that the incoming webhook call came from Bitbucket.
+  This means that an attacker could spoof calls to Atlantis and cause it to perform malicious actions.
+  :::
+  
+* ### `--checkout-strategy`
+  ```bash
+  atlantis server --checkout-strategy="<branch|merge>"
+  ```
+  How to check out pull requests.
+  Defaults to `branch`. See [Checkout Strategy](checkout-strategy.html) for more details.
+  
+* ### `--config`
+  ```bash
+  atlantis server --config="my/config/file.yaml"
+  ```
+  YAML config file where flags can also be set. See [Config File](#config-file) for more details.
+
+* ### `--data-dir`
+  ```bash
+  atlantis server --data-dir="path/to/data/dir"
+  ```
+  Directory where Atlantis will store its data. Will be created if it doesn't exist.
+  Defaults to `~/.atlantis`. Atlantis will store its database, checked out repos, Terraform plans and downloaded
+  Terraform binaries here. If Atlantis loses this directory, [locks](locking.html)
+  will be lost and unapplied plans will be lost.
+  
+* ### `--default-tf-version`
+  ```bash
+  atlantis server --default-tf-version="v0.12.0"
+  ```
+  Terraform version to default to. Will download to `<data-dir>/bin/terraform<version>`
+  if not in `PATH`. See [Terraform Versions](terraform-versions.html) for more details.
+
+* ### `--gh-hostname`
+  ```bash
+  atlantis server --gh-hostname="my.github.enterprise.com"
+  ```
+  Hostname of your GitHub Enterprise installation. If using [Github.com](https://github.com),
+  don't set. Defaults to `github.com`.
+  
+* ### `--gh-token`
+  ```bash
+  atlantis server --gh-token="token"
+  # or (recommended)
+  ATLANTIS_GH_TOKEN='token' atlantis server
+  ```
+  GitHub token of API user.
+
+* ### `--gh-user`
+  ```bash
+  atlantis server --gh-user="myuser"
+  ```
+   GitHub username of API user.
+  
+* ### `--gh-webhook-secret`
+  ```bash
+  atlantis server --gh-webhook-secret="secret"
+  # or (recommended)
+  ATLANTIS_GH_WEBHOOK_SECRET='secret' atlantis server
+  ```
+  Secret used to validate GitHub webhooks (see [https://developer.github.com/webhooks/securing/](https://developer.github.com/webhooks/securing/)).
+  
+  ::: warning SECURITY WARNING
+  If not specified, Atlantis won't be able to validate that the incoming webhook call came from GitHub.
+  This means that an attacker could spoof calls to Atlantis and cause it to perform malicious actions.
+  :::
+
+* ### `--gitlab-hostname`
+  ```bash
+  atlantis server --gitlab-hostname="my.gitlab.enterprise.com"
+  ```
+  Hostname of your GitLab Enterprise installation. If using [Gitlab.com](https://gitlab.com),
+  don't set. Defaults to `gitlab.com`.
+  
+* ### `--gitlab-token`
+  ```bash
+  atlantis server --gitlab-token="token"
+  # or (recommended)
+  ATLANTIS_GITLAB_TOKEN='token' atlantis server
+  ```
+  GitLab token of API user.
+
+* ### `--gitlab-user`
+  ```bash
+  atlantis server --gitlab-user="myuser"
+  ```
+   GitLab username of API user.
+  
+* ### `--gitlab-webhook-secret`
+  ```bash
+  atlantis server --gh-webhook-secret="secret"
+  # or (recommended)
+  ATLANTIS_GITLAB_WEBHOOK_SECRET='secret' atlantis server
+  ```
+  Secret used to validate GitLab webhooks.
+  
+  ::: warning SECURITY WARNING
+  If not specified, Atlantis won't be able to validate that the incoming webhook call came from GitLab.
+  This means that an attacker could spoof calls to Atlantis and cause it to perform malicious actions.
+  :::
+  
+* ### `--help`
+  ```bash
+  atlantis server --help
+  ```
+  View help.
+
+* ### `--log-level`
+  ```bash
+  atlantis server --log-level="<debug|info|warn|error>"
+  ```
+  Log level. Defaults to `info`.
+
+* ### `--port`
+  ```bash
+  atlantis server --port=8080
+  ```
+  Port to bind to. Defaults to `4141`.
+  
+* ### `--repo-config`
+  ```bash
+  atlantis server --repo-config="path/to/repos.yaml"
+  ```
+  Path to a YAML server-side repo config file. See [Server Side Repo Config](server-side-repo-config.html).
+
+* ### `--repo-config-json`
+  ```bash
+  atlantis server --repo-config-json='{"repos":[{"id":"/.*/", "apply_requirements":["mergeable"]}]}'
+  ```
+  Specify server-side repo config as a JSON string. Useful if you don't want to write a config file to disk.
+  See [Server Side Repo Config](server-side-repo-config.html) for more details.
+  
+  ::: tip
+  If specifying a [Workflow](custom-workflows.html#reference), [step](custom-workflows.html#step)'s
+  can be specified as follows:
+  ```json
+  {
+    "repos": [],
+    "workflows": {
+      "custom": {
+        "plan": {
+          "steps": [
+            "init",
+            {
+              "plan": {
+                "extra_args": ["extra", "args"]
+              }
+            },
+            {
+              "run": "my custom command"
+            }
+          ]
+        }
+      }
+    }
+  }
+  ```
+  :::
+  
+* ### `--repo-whitelist`
+  ```bash
+  # NOTE: Use single quotes to avoid shell expansion of *.
+  atlantis server --repo-whitelist='github.com/myorg/*'
+  ```
+  Atlantis requires you to specify a whitelist of repositories it will accept webhooks from.
+
+  Notes:
+  * Accepts a comma separated list, ex. `definition1,definition2`
+  * Format is `{hostname}/{owner}/{repo}`, ex. `github.com/runatlantis/atlantis`
+  * `*` matches any characters, ex. `github.com/runatlantis/*` will match all repos in the runatlantis organization
+  * For Bitbucket Server: `{hostname}` is the domain without scheme and port, `{owner}` is the name of the project (not the key), and `{repo}` is the repo name
+
+  Examples:
+  * Whitelist `myorg/repo1` and `myorg/repo2` on `github.com`
+    * `--repo-whitelist=github.com/myorg/repo1,github.com/myorg/repo2`
+  * Whitelist all repos under `myorg` on `github.com`
+    * `--repo-whitelist='github.com/myorg/*'`
+  * Whitelist all repos in my GitHub Enterprise installation
+    * `--repo-whitelist='github.yourcompany.com/*'`
+  * Whitelist all repositories
+    * `--repo-whitelist='*'`
+  
+* ### `--require-approval`
+  <Badge text="Deprecated" type="warn"/>
+  ```bash
+  atlantis server --require-approval
+  ```
+  This flag is deprecated. It requires all pull requests to be approved
+  before `atlantis apply` is allowed. See [Apply Requirements](apply-requirements.html) for more details.
+  
+  Instead of using this flag, create a server-side `--repo-config` file:
+  ```yaml
+  # repos.yaml
+  repos:
+  - id: /.*/
+    apply_requirements: [approved]
+  ```
+  Or use `--repo-config-json='{"repos":[{"id":"/.*/", "apply_requirements":["approved"]}]}'` instead.
+  
+* ### `--require-mergeable`
+  <Badge text="Deprecated" type="warn"/>
+  ```bash
+  atlantis server --require-mergeable
+  ```
+  This flag is deprecated. It causes all pull requests to be mergeable
+  before `atlantis apply` is allowed. See [Apply Requirements](apply-requirements.html) for more details.
+  
+  Instead of using this flag, create a server-side `--repo-config` file:
+  ```yaml
+  # repos.yaml
+  repos:
+  - id: /.*/
+    apply_requirements: [mergeable]
+  ```
+  Or use `--repo-config-json='{"repos":[{"id":"/.*/", "apply_requirements":["mergeable"]}]}'` instead.
+  
+* ### `--silence-whitelist-errors`
+  ```bash
+  atlantis server --silence-whitelist-errors
+  ```
+  Some users use the `--repo-whitelist` flag to control which repos Atlantis
+  responds to. Normally, if Atlantis receives a pull request webhook from a repo not listed
+  in the whitelist, it will comment back with an error. This flag disables that commenting.
+
+  Some users find this useful because they prefer to add the Atlantis webhook
+  at an organization level rather than on each repo.
+
+* ### `--slack-token`
+  ```bash
+  atlantis server --slack-token=token
+  # or (recommended)
+  ATLANTIS_SLACK_TOKEN='token' atlantis server
+  ```
+  API token for Slack notifications. Slack is not fully supported. TODO: Slack docs.
+
+* ### `--ssl-cert-file`
+  ```bash
+  atlantis server --ssl-cert-file="/etc/ssl/certs/my-cert.crt"
+  ```
+  File containing x509 Certificate used for serving HTTPS.
+  If the cert is signed by a CA, the file should be the concatenation
+  of the server's certificate, any intermediates, and the CA's certificate.
+  
+* ### `--ssl-key-file`
+  ```bash
+  atlantis server --ssl-cert-file="/etc/ssl/private/my-cert.key"
+  ```
+  File containing x509 private key matching `--ssl-cert-file`.
+  
+* ### `--tfe-token`
+  ```bash
+  atlantis server --tfe-token="xxx.atlasv1.yyy"
+  # or (recommended)
+  ATLANTIS_TFE_TOKEN='xxx.atlasv1.yyy' atlantis server
+  ```
+  A token for Terraform Enterprise integration. See [Terraform Enterprise](terraform-enterprise.html) for more details.
diff --git a/runatlantis.io/docs/server-side-repo-config.md b/runatlantis.io/docs/server-side-repo-config.md
index 6154d0b16..1c59f456f 100644
--- a/runatlantis.io/docs/server-side-repo-config.md
+++ b/runatlantis.io/docs/server-side-repo-config.md
@@ -14,6 +14,11 @@ Read through the [use-cases](#use-cases) to determine if you need it.
 To use server side repo config create a config file, ex. `repos.yaml`, and pass it to
 the `atlantis server` command via the `--repo-config` flag, ex. `--repo-config=path/to/repos.yaml`. 
 
+If you don't wish to write a config file to disk, you can use the
+`--repo-config-json` flag or `ATLANTIS_REPO_CONFIG_JSON` environment variable
+to specify your config as JSON. See [--repo-config-json](server-configuration.html#repo-config-json)
+for an example.
+
 ## Example Server Side Repo
 ```yaml
 # repos lists the config for specific repos.