mcp server is not available in Claude Code after install

[razenpok]

As per Quick Start, I ran the commands and restarted Claude Code after them:

tar xzf codebase-memory-mcp-*.tar.gz
mv codebase-memory-mcp ~/.local/bin/
codebase-memory-mcp install

codebase-memory-mcp is not available in /mcp

MacOS Tahoe 26.3.1

[razenpok]

razen@mac crimson-webgl % cat ~/.claude/.mcp.json
{
    "mcpServers": {
        "codebase-memory-mcp": {
            "command": "/Users/razen/.local/bin/codebase-memory-mcp"
        }
    }
}
razen@mac crimson-webgl % echo '{}' | /Users/razen/.local/bin/codebase-memory-mcp
level=info msg=mem.init budget_mb=24576 total_ram_mb=49152
level=info msg=server.start version=0.5.3
level=warn msg=ui.no_assets hint=rebuild with: make -f Makefile.cbm cbm-with-ui
level=info msg=watcher.start interval_ms=multi-sec
{"jsonrpc":"2.0","id":0,"error":{"code":-32700,"message":"Parse error"}}
level=info msg=server.shutdown
level=info msg=watcher.stop

[DeusData]

Could you verify a few things?

1. Is the binary on your PATH? Run: which codebase-memory-mcp
2. Does codebase-memory-mcp --version work?
3. Check if the MCP config was created: cat ~/.claude/.mcp.json
4. Try restarting Claude Code completely (quit and reopen, not just reload)

The install command writes to ~/.claude/.mcp.json which Claude Code reads on startup. If the file exists with the correct binary path and Claude Code was fully restarted, it should appear in /mcp.

Also: we recently removed the repo-level .mcp.json (it had a hardcoded path). Make sure you're using the version installed via codebase-memory-mcp install, not a stale repo config.

[razenpok]

razen@mac crimson-webgl % which codebase-memory-mcp
/Users/razen/.local/bin/codebase-memory-mcp
razen@mac crimson-webgl % codebase-memory-mcp --version
codebase-memory-mcp 0.5.3
razen@mac crimson-webgl % cat ~/.claude/.mcp.json
{
    "mcpServers": {
        "codebase-memory-mcp": {
            "command": "/Users/razen/.local/bin/codebase-memory-mcp"
        }
    }
}

razen@mac crimson-webgl % claude mcp list
Checking MCP server health...

claude.ai Gmail: https://gmail.mcp.claude.com/mcp - ✓ Connected
claude.ai Google Calendar: https://gcal.mcp.claude.com/mcp - ✓ Connected

It looks like claude code ignores ~/.claude/.mcp.json?

[razenpok]

If I copy .mcp.json to the project folder, it gets picked up, but it gets stuck in the "connecting" state

[Divere]

same, last version of claude code doesn't work

[williamwissemann]

I have been bumping into the same issue since yesterday; it's just stuck connecting.

[indy-singh]

Yep, exactly the same here.

>cat %userprofile%\.claude\settings.json
{
        "enabledPlugins": {
                "csharp-lsp@claude-plugins-official": true,
                "ast-grep@ast-grep-marketplace": true,
                "code-review-graph@code-review-graph": true
        },
        "extraKnownMarketplaces": {
                "ast-grep-marketplace": {
                        "source": {
                                "source": "github",
                                "repo": "ast-grep/agent-skill"
                        }
                },
                "code-review-graph": {
                        "source": {
                                "source": "github",
                                "repo": "tirth8205/code-review-graph"
                        }
                }
        },
        "autoUpdatesChannel": "latest",
        "skipDangerousModePermissionPrompt": true,
        "mcpServers": {
                "codebase-memory-mcp": {
                        "type": "stdio",
                        "command": "C:\\Users\\REDACTED\\AppData\\Local\\codebase-memory-mcp\\codebase-memory-mcp.exe"
                }
        }
}

Then

>cat %userprofile%\.claude\.mcp.json
{
        "mcpServers": {
                "codebase-memory-mcp": {
                        "type": "stdio",
                        "command": "C:\\Users\\REDACTED\\AppData\\Local\\codebase-memory-mcp\\codebase-memory-mcp.exe"
                }
        }
}

Then

>where codebase-memory-mcp
C:\Users\REDACTED\AppData\Local\codebase-memory-mcp\codebase-memory-mcp.exe

Then

>codebase-memory-mcp.exe --version
codebase-memory-mcp 0.5.4

[indy-singh]

Finally got it to work:-

set HOME=%USERPROFILE%
codebase-memory-mcp install

That places a file in "C:\Users\REDACTED\.claude.json" which I then tweaked to use the path var:-

{
...trunc
	"feedbackSurveyState": {
		"lastShownTime": 1773704779926
	},
	"lastPlanModeUse": 1773956222556,
	"mcpServers": {
		"codebase-memory-mcp": {
			"command": "codebase-memory-mcp"
		}
	}
}

The pwsh script didn't work and just doing codebase-memory-mcp install gave me the error error: HOME not set.

I guess the binary needs to be updated to use %USERPROFILE% on Windows?

[DeusData]

@razenpok Is this still happening on v0.5.5?

Since your report, we've made two changes that may have fixed this:

1. Dual MCP config location — install now writes to both ~/.claude/.mcp.json and ~/.claude.json (Claude Code >=2.1.80 changed the config path)
2. VS Code compatibility fixes — proper protocol version negotiation and schema validation

If you're still experiencing this, could you share:

• Which version you're running (codebase-memory-mcp --version)
• Which editor/agent you're using
• The output of cat ~/.claude.json (or ~/.claude/.mcp.json)

[cristicalin]

@DeusData I have the same problem.

Just tested with codebase-memory-mcp version 0.5.5 (cli version, w/o ui) and claude code 2.1.81.

cat ~/.claude.json | jq .mcpServers
{
  "codebase-memory-mcp": {
    "command": "/Users/kman/.local/bin/codebase-memory-mcp"
  }
}

cat ~/.claude/.mcp.json | jq .mcpServers
{
  "codebase-memory-mcp": {
    "command": "/Users/kman/.local/bin/codebase-memory-mcp"
  }
}

/Users/kman/.local/bin/codebase-memory-mcp --version
codebase-memory-mcp 0.5.5

[cristicalin]

I tested a fix proposed in #109 (comment) which seems to work. Note this was only tested on macOS and it's generated by claude and only tested with claude code.

[Zorato]

I have problem on Claude Code v2.1.74 (I'm on stable release channel) and Codebase momery mcp v0.5.5:

• In /mcp list it shows as connected:

User MCPs (/Users/username/.claude.json)
    codebase-memory-mcp · ✔ connected
    jetbrains · ✔ connected

• when asked to index project:

 index this project                                                                                                                                                                                                                               
                                                                                                                                                                                                                                                   
⏺ Skill(codebase-memory-reference)                                                                                                                                                                                                                 
  ⎿  Successfully loaded skill                                                                                                                                                                                                                     
                                                                                                                                                                                                                                                   
⏺ The codebase-memory-mcp tools don't appear to be available in this session — the server may not be connected. You can check with /mcp to see which MCP servers are active and reconnect if needed. 

Or like this:

index this project                                                                                                                                                                                                                               
                                                                                                                                                                                                                                                   
⏺ Skill(codebase-memory-exploring)                                                                                                                                                                                                                 
  ⎿  Successfully loaded skill                                                                                                                                                                                                                     
                                                                                                                                                                                                                                                   
⏺ The codebase-memory-mcp tools don't appear to be available in the current MCP server list. The /mcp command showed it reconnected, but the tools aren't being exposed.                                                                           
                                                                                                                                                                                                                                                   
  You can check the MCP connection status by running /mcp again, or verify the server is properly configured in your Claude Code settings. The codebase-memory-mcp server needs to be running and registered for index_repository to be available. 

Even though terminal/claude code/mcp connection was restarted a few times.
Thi binary is in-place and running ok:

% codebase-memory-mcp --version
codebase-memory-mcp 0.5.5

[Auuufff]

any updates on that? have the same issue

Claude Code v2.1.81
codebase-memory-mcp 0.5.5