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fix: don't set COPILOT_HOME, and provide MCP instructions instead #286

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fix: don't set COPILOT_HOME, and provide MCP instructions instead #286

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5006202
fix: don't set COPILOT_HOME, and provide MCP instructions instead
wdconinc May 14, 2026
802c33d
fix: close code fence
wdconinc May 14, 2026
b5286de
fix: install all of copilot/ into /etc/copilot
wdconinc May 14, 2026
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6 changes: 2 additions & 4 deletions containers/eic/Dockerfile
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Expand Up @@ -376,10 +376,8 @@ COPY eic-env.sh /etc/eic-env.sh
COPY profile.d/* /etc/profile.d
COPY singularity.d /.singularity.d

## System-level Copilot MCP server defaults.
## /opt/local/bin/xrootd-mcp-server is the Spack view path for the
## xrootd-mcp-server package (installed like github-copilot via npm --global).
COPY copilot/mcp-config.json /etc/copilot/mcp-config.json
## System-level Copilot server defaults.
COPY copilot/ /etc/copilot/

## set ROOT TFile forward compatibility
RUN sed --in-place --follow-symlinks 's/# \(TFile.v630forwardCompatibility:\) no/\1 yes/' /opt/local/etc/root/system.rootrc
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42 changes: 42 additions & 0 deletions containers/eic/copilot/mcp-config.instructions.md
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@@ -0,0 +1,42 @@
## Container Environment: Available MCP Servers
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This session is running inside a container that has the following MCP servers
pre-installed and ready to use. They are **not active by default** — the user
must add them to their personal configuration once.
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### Available servers

| Name | Description |
|------|-------------|
| `eic-xrootd-mcp-server` | Access EIC data via XRootD from the JLab data transfer node (`root://dtn-eic.jlab.org`) |
| `eic-zenodo-mcp-server` | Browse and retrieve EIC datasets and publications from Zenodo (`https://zenodo.org`) |

### How to enable

If the user asks about EIC data, simulation inputs, published datasets, or anything
that would benefit from remote file or repository access, suggest they enable the
relevant server(s) by editing `~/.copilot/mcp-config.json`.

If the file does not exist, create it. Add or merge the following:

```json
{
"mcpServers": {
"eic-xrootd-mcp-server": {
"command": "/opt/local/bin/xrootd-mcp-server",
"env": {
"XROOTD_SERVER": "root://dtn-eic.jlab.org"
}
},
"eic-zenodo-mcp-server": {
"command": "/opt/local/bin/zenodo-mcp-server",
"env": {
"ZENODO_BASE_URL": "https://zenodo.org"
}
}
}
}
```

After saving the file, run /mcp show to confirm the servers are active. The configuration persists across
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sessions in the user's home directory.
14 changes: 6 additions & 8 deletions containers/eic/profile.d/z23_copilot_mcp.sh
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@@ -1,18 +1,16 @@
#!/bin/sh

## Set COPILOT_HOME to /etc/copilot so github-copilot reads MCP server
## configuration directly from the system-level config, rather than from
## ~/.copilot. This works for Singularity/Apptainer users whose home
## directory is bind-mounted from the host at runtime.
## Set COPILOT_CUSTOM_INSTRUCTIONS_DIRS to /etc/copilot so github-copilot
## reads custom instructions with a pointer to MCP server configuration.
##
## To revert to ~/.copilot (or any other directory), add the following
## to your ~/.bashrc:
## unset COPILOT_HOME
## unset COPILOT_CUSTOM_INSTRUCTIONS_DIRS

if [ -z "${COPILOT_HOME:-}" ]; then
export COPILOT_HOME=/etc/copilot
if [ -z "${COPILOT_CUSTOM_INSTRUCTIONS_DIRS:-}" ]; then
export COPILOT_CUSTOM_INSTRUCTIONS_DIRS=/etc/copilot
else
case "$-" in
*i*) printf '%s\n' "Note: COPILOT_HOME is already set to '${COPILOT_HOME}'; not overriding with /etc/copilot." >&2 ;;
*i*) printf '%s\n' "Note: COPILOT_CUSTOM_INSTRUCTIONS_DIRS is already set to '${COPILOT_CUSTOM_INSTRUCTIONS_DIRS}'; not overriding with /etc/copilot." >&2 ;;
esac
fi
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