Where does the bug appear (feature/product)?
Cursor IDE
Describe the Bug
Where does the bug appear?
MCP / Cursor Plugins / Agent tool discovery
Describe the Bug:
After updating Cursor from 3.2.11 to 3.2.16, the Atlassian MCP server still connects and its Jira tools are callable, but Cursor no longer writes the Atlassian tool schemas into the project MCP filesystem.
This breaks agent workflows that are instructed to discover MCP tools by reading:
~/.cursor/projects//mcps/plugin-atlassian-atlassian/tools/*.json
Before the update, the same workspace had descriptors like:
- getAccessibleAtlassianResources.json
- getJiraIssue.json
- searchJiraIssuesUsingJql.json
- searchAtlassian.json
- fetchAtlassian.json
After the update/re-auth, the local descriptor folder has no tools directory and only widget resources: - resources/jira-widget-openai.json
- resources/jira-widget-ext-apps.json
- resources/confluence-widget-openai.json
- resources/confluence-widget-ext-apps.json
However, direct MCP calls still work. I verified that these tools execute successfully: - getAccessibleAtlassianResources
- getJiraIssue
- searchJiraIssuesUsingJql
So the live MCP server is healthy; the regression appears to be in Cursor’s MCP filesystem writer / tool descriptor discovery.
Actual Behavior:
Cursor writes zero Atlassian tools to the local MCP filesystem, causing fresh agents to conclude that Jira tools are unavailable and fall back to browser/manual Jira access.
Evidence:
Before:
- Cursor 3.2.11
- Logs showed Atlassian toolCount: 31-32
- Prior sessions successfully read:
mcps/plugin-atlassian-atlassian/tools/getJiraIssue.json
After: - Cursor 3.2.16
- Logs show:
toolCount: 0 for plugin-atlassian-atlassian after reconnect - Local MCP folder contains only widget resources, no tools directory
- Direct CallMcpTool calls to getJiraIssue and searchJiraIssuesUsingJql still work
Relevant log excerpts: - 2026-04-28: toolCount 31/32 for plugin-atlassian-atlassian
- 2026-04-29 after update/restart: Cursor 3.2.16
- 2026-04-29 13:33:32: plugin-atlassian-atlassian connected, but MCP FileSystem Writer wrote toolCount: 0
Operating System:
macOS / Darwin arm64 25.3.0
Version Information:
Cursor 3.2.16 stable
Previous working version in logs: Cursor 3.2.11
Does this stop you from using Cursor?
No - Cursor works, but MCP/Jira workflows regress for fresh agents because tool discovery is broken.
Additional Information:
This seems related to earlier MCP tool-injection/discovery bugs, but it is not exactly the same failure mode: the tools are still callable if the agent already knows the tool names and schemas. The broken part is the local tool descriptor filesystem used for agent discovery.
Steps to Reproduce
- Use Cursor with the Atlassian plugin/MCP enabled.
- Authenticate Atlassian MCP.
- Ask an agent to fetch Jira context from a ticket key, e.g. KEY-1234.
- The agent checks the local MCP descriptor path:
~/.cursor/projects//mcps/plugin-atlassian-atlassian/tools - Observe that the tools directory is missing or has zero Jira tools.
- Directly calling known Atlassian MCP tools still succeeds, proving the MCP server is connected and functional.
Expected Behavior
When Atlassian MCP is connected and tools are callable, Cursor should also expose/write the corresponding tool schema descriptors into the project MCP filesystem, so agents can discover and call them reliably.
Operating System
MacOS
Version Information
Version: 3.2.16 (Universal)
VSCode Version: 1.105.1
Commit: 3e548838cf824b70851dd3ef27d0c6aae371b3f0
Date: 2026-04-28T21:07:47.682Z (14 hrs ago)
Layout: glass
Build Type: Stable
Release Track: Default
Electron: 39.8.1
Chromium: 142.0.7444.265
Node.js: 22.22.1
V8: 14.2.231.22-electron.0
OS: Darwin arm64 25.3.0
Does this stop you from using Cursor
No - Cursor works, but with this issue
