From ebac26222acc8a6317ccfb0b6ef6cbd261ab51c6 Mon Sep 17 00:00:00 2001
From: Man Yue Mo <mmo@semmle.com>
Date: Thu, 9 Oct 2025 15:45:07 +0000
Subject: [PATCH 1/2] Use remote github mcp server

---
 taskflows/examples/example_large_list_result_iter.yaml | 2 +-
 toolboxes/github_official.yaml                         | 9 ++++-----
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/taskflows/examples/example_large_list_result_iter.yaml b/taskflows/examples/example_large_list_result_iter.yaml
index b94c713..bb0ae87 100644
--- a/taskflows/examples/example_large_list_result_iter.yaml
+++ b/taskflows/examples/example_large_list_result_iter.yaml
@@ -17,6 +17,6 @@ taskflow:
       must_complete: true
       repeat_prompt: true
       agents:
-        - echo
+        - assistant
       user_prompt: |
         Echo this:  The title is {{ RESULT_title }} and the url is {{ RESULT_url }}.
diff --git a/toolboxes/github_official.yaml b/toolboxes/github_official.yaml
index 0321281..e1cde32 100644
--- a/toolboxes/github_official.yaml
+++ b/toolboxes/github_official.yaml
@@ -3,8 +3,7 @@ seclab-taskflow-agent:
   version: 1
 
 server_params:
-  kind: stdio
-  command: docker
-  args: ["run", "-i", "--rm", "-e", "GITHUB_PERSONAL_ACCESS_TOKEN", "ghcr.io/github/github-mcp-server"]
-  env:
-    GITHUB_PERSONAL_ACCESS_TOKEN: "{{ env GITHUB_PERSONAL_ACCESS_TOKEN }}"
+  kind: streamable
+  url: https://api.githubcopilot.com/mcp/
+  headers:
+    Authorization: "{{ env GITHUB_AUTH_HEADER }}"
\ No newline at end of file

From f82c69ba191f08e281ab1f263819e4ebeb25bdd5 Mon Sep 17 00:00:00 2001
From: Man Yue Mo <mmo@semmle.com>
Date: Thu, 9 Oct 2025 15:48:30 +0000
Subject: [PATCH 2/2] Remove socket from run script, change README and fix some
 typos

---
 README.md     | 19 ++-----------------
 docker/run.sh |  1 -
 2 files changed, 2 insertions(+), 18 deletions(-)

diff --git a/README.md b/README.md
index 6f53bd3..7452f9f 100644
--- a/README.md
+++ b/README.md
@@ -115,23 +115,21 @@ MY_TASKFLOWS=~/my_taskflows MY_DATA=~/codeql_databases CODEQL_DBS_BASE_PATH=/app
 
 For more advanced scenarios like e.g. making custom MCP server code available, you can alter the run script to mount your custom code into the image and configure your toolboxes to use said code accordingly.
 
-Example: a custom MCP server deployment via Docker image:
-
 ```sh
 export MY_MCP_SERVERS="$PWD"/mcp_servers
 export MY_TOOLBOXES="$PWD"/toolboxes
 export MY_PERSONALITIES="$PWD"/personalities
 export MY_TASKFLOWS="$PWD"/taskflows
 export MY_PROMPTS="$PWD"/prompts
+export MY_DATA="$PWD"/data
 
 if [ ! -f ".env" ]; then
     touch ".env"
 fi
 
 docker run \
-       --volume /var/run/docker.sock:/var/run/docker.sock \
        --volume "$PWD"/logs:/app/logs \
-       --mount type=bind,src="$PWD"/env,dst=/app/.env,ro \
+       --mount type=bind,src="$PWD"/.env,dst=/app/.env,ro \
        ${MY_DATA:+--mount type=bind,src=$MY_DATA,dst=/app/my_data} \
        ${MY_MCP_SERVERS:+--mount type=bind,src=$MY_MCP_SERVERS,dst=/app/my_mcp_servers,ro} \
        ${MY_TASKFLOWS:+--mount type=bind,src=$MY_TASKFLOWS,dst=/app/taskflows/my_taskflows,ro} \
@@ -141,19 +139,6 @@ docker run \
        "ghcr.io/githubsecuritylab/seclab-taskflow-agent" "$@"
 ```
 
-Our default run script makes the Docker socket available to the image, which contains the Docker cli, so 3rd party Docker based stdio MCP servers also function as normal.
-
-Example: a toolbox configuration using the official GitHub MCP Server via Docker:
-
-```yaml
-server_params:
-  kind: stdio
-  command: docker
-  args: ["run", "-i", "--rm", "-e", "GITHUB_PERSONAL_ACCESS_TOKEN", "ghcr.io/github/github-mcp-server"]
-  env:
-    GITHUB_PERSONAL_ACCESS_TOKEN: "{{ env GITHUB_PERSONAL_ACCESS_TOKEN }}"
-```
-
 ## Personalities
 
 Core characteristics for a single Agent. Configured through YAML files in `personalities/`.
diff --git a/docker/run.sh b/docker/run.sh
index 798a450..4e77ad4 100755
--- a/docker/run.sh
+++ b/docker/run.sh
@@ -5,7 +5,6 @@ if [ ! -f ".env" ]; then
 fi
 docker run -i \
        --platform linux/amd64 \
-       --volume /var/run/docker.sock:/var/run/docker.sock \
        --volume "$PWD/"logs:/app/logs \
        --mount type=bind,src="$PWD/".env,dst=/app/.env,ro \
        ${MY_DATA:+--mount type=bind,src=$MY_DATA,dst=/app/my_data} \