Source code files corrupted when server/tool attempts to base64 encode my files on read and write #841
Description
Describe the bug
I had an awesome day with GPT 5.0 and a more sophisticated prompt/spec that would do multi change batches with Github MCP, but in the end my files got corrupted. It was corrupted because the MCP seems to only work with base64 blobs and not actual text/code files from github (), and then it writes base64 back over my code files. Details below. I don't know if it matters (validating now) but I was using today's new GPT 5.0 preview.
Detailed response from agent mode
Cannot safely rewrite all remote main.bicep files here because I only have the base64 blobs (and the raw fetch tool returns truncated snippets with ellipses), so producing full, exact, whitespace‑preserving replacements (removing just the single deprecated output line) risks introducing corruption similar to the earlier csproj issue.
Summary of findings:
All sampled dotnet templates (eventgrid-blob, dotnet-sql) still contain: output APPLICATIONINSIGHTS_CONNECTION_STRING string = monitoring.outputs.connectionString
Likely present in the other language templates too (pattern is consistent across these AZD samples).
Root cause of earlier miss:
Infra removal step never executed; workflow focused only on csproj/package edits; no audit pass enforced absence of the output.
Steps to reproduce the behavior
- Run the prompt spec above
- Observe commits made by Github MCP server. See already done examples above.
Expected vs actual behavior
These are just source code files (xml, json, js) so text should come in and text should go out. Never base64.
Logs
Tool Call - call_nldxATetAhrrZMmutwn6wRL6__vscode-1754595944293
Request
id : call_nldxATetAhrrZMmutwn6wRL6__vscode-1754595944293
tool : mcp_github_get_file_contents
args : {
"owner": "Azure-Samples",
"repo": "functions-quickstart-dotnet-azd-eventgrid-blob",
"path": "src/src.csproj",
"branch": "main"
}
Response
{"type":"file","encoding":"base64","size":1482,"name":"src.csproj","path":"src/src.csproj","content":"77u/PFByb2plY3QgU2RrPSJNaWNyb3NvZnQuTkVULlNkayI+CiAgPFByb3Bl\ncnR5R3JvdXA+CiAgICA8VGFyZ2V0RnJhbWV3b3JrPm5ldDguMDwvVGFyZ2V0\nRnJhbWV3b3JrPgogICAgPEF6dXJlRnVuY3Rpb25zVmVyc2lvbj52NDwvQXp1\ncmVGdW5jdGlvbnNWZXJzaW9uPgogICAgPE91dHB1dFR5cGU+RXhlPC9PdXRw\ndXRUeXBlPgogICAgPEltcGxpY2l0VXNpbmdzPmVuYWJsZTwvSW1wbGljaXRV\nc2luZ3M+CiAgICA8TnVsbGFibGU+ZW5hYmxlPC9OdWxsYWJsZT4KICAgIDxV\nc2VyU2VjcmV0c0lkPjc2MzM5NGRmLWI4MDctNGY4Mi04ZTUwLTI1MTZlNDBj\nM2M1YjwvVXNlclNlY3JldHNJZD4KICA8L1Byb3BlcnR5R3JvdXA+CiAgPEl0\nZW1Hcm91cD4KICAgIDxGcmFtZXdvcmtSZWZlcmVuY2UgSW5jbHVkZT0iTWlj\ncm9zb2Z0LkFzcE5ldENvcmUuQXBwIiAvPgogICAgPFBhY2thZ2VSZWZlcmVu\nY2UgSW5jbHVkZT0iTWljcm9zb2Z0LkFwcGxpY2F0aW9uSW5zaWdodHMuV29y\na2VyU2VydmljZSIgVmVyc2lvbj0iMi4yMy4wIiAvPiAKICAgIDxQYWNrYWdl\nUmVmZXJlbmNlIEluY2x1ZGU9Ik1pY3Jvc29mdC5BenVyZS5GdW5jdGlvbnMu\nV29ya2VyLkFwcGxpY2F0aW9uSW5zaWdodHMiIFZlcnNpb249IjIuMC4wIiAv\nPiAKICAgIDxQYWNrYWdlUmVmZXJlbmNlIEluY2x1ZGU9Ik1pY3Jvc29mdC5B\nenVyZS5GdW5jdGlvbnMuV29ya2VyIiBWZXJzaW9uPSIyLjAuMCIgLz4KICAg\nIDxQYWNrYWdlUmVmZXJlbmNlIEluY2x1ZGU9Ik1pY3Jvc29mdC5BenVyZS5G\ndW5jdGlvbnMuV29ya2VyLkV4dGVuc2lvbnMuSHR0cC5Bc3BOZXRDb3JlIiBW\nZXJzaW9uPSIyLjAuMSIgLz4KICAgIDxQYWNrYWdlUmVmZXJlbmNlIEluY2x1\nZGU9Ik1pY3Jvc29mdC5BenVyZS5GdW5jdGlvbnMuV29ya2VyLkV4dGVuc2lv\nbnMuU3RvcmFnZS5CbG9icyIgVmVyc2lvbj0iNi42LjEiIC8+CiAgICA8UGFj\na2FnZVJlZmVyZW5jZSBJbmNsdWRlPSJNaWNyb3NvZnQuQXp1cmUuRnVuY3Rp\nb25zLldvcmtlci5TZGsiIFZlcnNpb249IjIuMC4yIiAvPgogIDwvSXRlbUdy\nb3VwPgogIDxJdGVtR3JvdXA+CiAgICA8Tm9uZSBVcGRhdGU9Imhvc3QuanNv\nbiI+CiAgICAgIDxDb3B5VG9PdXRwdXREaXJlY3Rvcnk+UHJlc2VydmVOZXdl\nc3Q8L0NvcHlUb091dHB1dERpcmVjdG9yeT4KICAgIDwvTm9uZT4KICAgIDxO\nb25lIFVwZGF0ZT0ibG9jYWwuc2V0dGluZ3MuanNvbiI+CiAgICAgIDxDb3B5\nVG9PdXRwdXREaXJlY3Rvcnk+UHJlc2VydmVOZXdlc3Q8L0NvcHlUb091dHB1\ndERpcmVjdG9yeT4KICAgICAgPENvcHlUb1B1Ymxpc2hEaXJlY3Rvcnk+TmV2\nZXI8L0NvcHlUb1B1Ymxpc2hEaXJlY3Rvcnk+CiAgICA8L05vbmU+CiAgPC9J\ndGVtR3JvdXA+CiAgPEl0ZW1Hcm91cD4KICAgIDxVc2luZyBJbmNsdWRlPSJT\neXN0ZW0uVGhyZWFkaW5nLkV4ZWN1dGlvbkNvbnRleHQiIEFsaWFzPSJFeGVj\ndXRpb25Db250ZXh0IiAvPgogIDwvSXRlbUdyb3VwPgo8L1Byb2plY3Q+\n","sha":"dfedb117726cf0cddfb5fe0f7964d7f60689299d","url":"https://api.github.com/repos/Azure-Samples/functions-quickstart-dotnet-azd-eventgrid-blob/contents/src/src.csproj?ref=main","git_url":"https://api.github.com/repos/Azure-Samples/functions-quickstart-dotnet-azd-eventgrid-blob/git/blobs/dfedb117726cf0cddfb5fe0f7964d7f60689299d","html_url":"https://github.com/Azure-Samples/functions-quickstart-dotnet-azd-eventgrid-blob/blob/main/src/src.csproj","download_url":"https://raw.githubusercontent.com/Azure-Samples/functions-quickstart-dotnet-azd-eventgrid-blob/main/src/src.csproj"}
Thinking