Completely unusable after botched upgrade

[dskvr]

Version

codebase-memory-mcp 0.8.1

Platform

Linux (x64)

Install channel

GitHub release archive / install.sh / install.ps1

Binary variant

standard

What happened, and what did you expect?

What happened: Installed via curl on active installation, botched everything, uninstalled via cli, reinstalled via install.sh, cannot add new indexes on fresh install.

Expected: install script would detect active installation and produce graceful path to upgrade.

See #607 and #608 for context

Reproduction

See #607

irrelevant. Hopefully this helps you fix this so others do not have this frustrating of an experience.

Standard pattern: install paths on active installations gracefully produce upgrade path; not uninstall path with broken state.

Logs

codebase-memory-mcp uninstall                                                                                       
codebase-memory-mcp uninstall

Claude Code: removed 0 skill(s)
  removed MCP config entry
  removed PreToolUse + SessionStart hooks
Codex CLI: removed MCP config entry
  removed instructions
Gemini CLI: removed MCP config + hooks + instructions
OpenCode: removed MCP config entry
  removed instructions
VS Code: removed MCP config entry
Cursor: removed MCP config entry
OpenClaw: removed MCP config entry
Kiro: removed MCP config entry

Found 1 index(es):
  /home/***/.cache/codebase-memory-mcp/_config.db
Delete these indexes? (y/n): y
Removed 1 index(es).
Removed /home/***/.local/bin/codebase-memory-mcp

Uninstall complete.
 ***@arch  ~  codebase-memory-mcp          
zsh: command not found: codebase-memory-mcp
 ✘ ***@arch  ~  curl -fsSL https://raw.githubusercontent.com/DeusData/codebase-memory-mcp/main/install.sh | bash -s -- --ui
codebase-memory-mcp installer
  os:      linux
  arch:    amd64
  variant: ui
  target:  /home/***/.local/bin/codebase-memory-mcp

Downloading codebase-memory-mcp-ui-linux-amd64-portable.tar.gz...
######################################################################## 100.0%
Checksum verified.
Extracting...
Installed: codebase-memory-mcp 0.8.1

Configuring coding agents...
codebase-memory-mcp install 0.8.1

pgrep: pattern that searches for process name longer than 15 characters will result in zero matches
Try `pgrep -f' option to match against the complete command line.
Detected agents: Claude-Code Codex Gemini-CLI OpenCode VS-Code Cursor OpenClaw Kiro

Claude Code:
  skills: 1 installed
  mcp: /home/***/.claude/.mcp.json
  mcp: /home/***/.claude.json
  hooks: PreToolUse (Grep/Glob search-graph augmenter, non-blocking)
  hooks: SessionStart (MCP usage reminder on startup/resume/clear/compact)
Codex CLI:
  mcp: /home/***/.codex/config.toml
  instructions: /home/***/.codex/AGENTS.md
  hooks: SessionStart (codebase-memory-mcp reminder)
Gemini CLI:
  mcp: /home/***/.gemini/settings.json
  instructions: /home/***/.gemini/GEMINI.md
  hooks: BeforeTool + SessionStart (codebase-memory-mcp reminder)
OpenCode:
  mcp: /home/***/.config/opencode/opencode.json
  instructions: /home/***/.config/opencode/AGENTS.md
VS Code:
  mcp: /home/***/.config/Code/User/mcp.json
Cursor:
  mcp: /home/***/.cursor/mcp.json
OpenClaw:
  mcp: /home/***/.openclaw/openclaw.json
Kiro:
  mcp: /home/***/.kiro/settings/mcp.json

PATH already includes /home/***/.local/bin

Install complete. Restart your shell or run:
  source /home/***/.zshrc

Done! Restart your coding agent to start using codebase-memory-mcp.

Project scale (if relevant)

250K, don't remember, you nuked my db

Confirmations

• I searched existing issues and this is not a duplicate.
• My reproduction uses shareable code (a dummy snippet or a public OSS repository), not proprietary code.

[kumayizxcvb]

This is a rough experience, sorry you hit this. The upgrade path clearly needs more defensive handling.

One thing that stands out from your logs: the uninstaller caught the _config.db in ~/.cache, but I'm wondering if there are residual state files elsewhere that survived the reinstall. Have you checked ~/.config/codebase-memory-mcp or ~/.local/share/codebase-memory-mcp for leftover data?

Also, when you say you "cannot add new indexes" on the fresh install—what specific error are you getting? Is it silently failing, throwing a permissions issue, or complaining about existing locks? That detail would help narrow down whether it's a stale file problem or something deeper in the install script logic.

The graceful upgrade expectation is completely reasonable, by the way. Hopefully the maintainers can address this soon.

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[DeusData]

Hey @dskvr, sorry for this experience. We usually try to catch this type of behavior through our smoke test suite, before it reaches the users. Seems like there is a gap. Will visit this as soon as possible and come back to you. With regards to dropping the indexes on update/install: Yes this is deliberate, as updated versions can have new extraction logic, which would change the graph and could potentially lead to unexpected behavior when incrementally indexing the graph with new versions. This is kinda the tradeoff, that you then need to reindex your project. If you have a suggestion on how to do it better, I am always open for feedback