install.sh aborts when agent harness tool config is a symlink instead of update the config #2671

Version

codebase-memory-mcp 0.12.1

Platform

macOS (Intel)

Install channel

GitHub release archive / install.sh / install.ps1

Binary variant

standard

What happened, and what did you expect?

Current:

install.sh downloads, verifies, and installs the binary fine, then fails during agent configuration if any harness config file is a symlink.

In my case /Users/sanath/Library/Application Support/Zed/settings.json is a symlink (dotfiles checkout pattern), and the Zed step fails:

error: agent_config agent=Zed op=mcp_install path=/Users/sanath/Library/Application Support/Zed/settings.json (target: regular file, 379 bytes)

That single failure aborts the whole activation:

error: one or more agent configurations failed; the published/current executable was kept, and PATH/index cleanup was not attempted
error: activation stopped after one or more agent configuration or cleanup operations failed; the published/current executable was kept, and configuration changes that completed may remain. Please restart your coding-agent sessions after resolving the errors above.

Expected:

a user-owned symlink should either be followed (like a normal config file — this is the common ln -s ~/dotfiles/... pattern) or skipped with a warning for that one agent. It should not fail the entire install, keep the old executable, skip PATH/index cleanup, and leave other agents' configs partially applied.

Secondary diagnostics issue: the path is a symlink (mcp: ... is a symlink per local ls -l), but the error detail says (target: regular file, 379 bytes). That hides the actual refusal reason and makes triage hard. Compare src/cli/cli.c:describe_agent_config_target() + src/cli/config_edit_path.c:edit_path_classify() — the fail-closed symlink policy and the cbm_path_info_utf8() (lstat-based, src/foundation/compat_fs.c) reporting seem to disagree here.

Reproduction

1. Code: N/A — installer bug, no repo to index. Config precondition:
   ls -l "/Users/sanath/Library/Application Support/Zed/settings.json" shows a symlink (e.g. settings.json -> ~/dotfiles/zed/settings.json, 379 bytes target).
2. Command: curl -fsSL https://raw.githubusercontent.com/DeusData/codebase-memory-mcp/main/install.sh | bash
3. Result: binary verified (Verified candidate: codebase-memory-mcp 0.12.1), agents detected, OpenCode/Antigravity/etc. configured, then Zed mcp_install errors and the whole activation stops with the two error: lines above.
   Expected: install succeeds; Zed entry is written through the symlink (or Zed is skipped with a warning and install still completes).

Workarounds tried: none yet — replacing the symlink with a regular file, or --clients=<list without zed> / --skip-config, would presumably bypass it but defeats dotfiles management.

Logs

codebase-memory-mcp installer
  os:      darwin
  arch:    amd64
  target:  /Users/sanath/.local/bin/codebase-memory-mcp

Downloading codebase-memory-mcp-darwin-amd64.tar.gz...
######################################################################## 100.0%
Checksum verified.
Extracting...
Fixing macOS code signing...
Verified candidate: codebase-memory-mcp 0.12.1
codebase-memory-mcp install 0.12.1

Found 1 existing index(es). Keeping them. After install, re-index to pick up this version's improvements:
  /Users/sanath/.cache/codebase-memory-mcp/activity.db

xattr: /tmp/cbm-install-Sp6XB1/codebase-memory-mcp: No such xattr: com.apple.quarantine
/tmp/cbm-install-Sp6XB1/codebase-memory-mcp: replacing existing signature
codebase-memory-mcp 0.12.1
Stopping active CBM sessions and operations for install...
Installed binary -> /Users/sanath/.local/bin/codebase-memory-mcp

Detected agents: Claude-Code Codex Gemini-CLI Zed OpenCode Antigravity KiloCode VS-Code Cursor Cline Copilot-CLI Factory-Droid Goose Grok-Build Kimi Code CLI Amp Devin CLI / Local Pi Oh My Pi (omp)

Antigravity:
  mcp: /Users/sanath/.gemini/config/mcp_config.json
  instructions: /Users/sanath/.gemini/GEMINI.md
Zed:
error: agent_config agent=Zed op=mcp_install path=/Users/sanath/Library/Application Support/Zed/settings.json (target: regular file, 379 bytes)
  mcp: /Users/sanath/Library/Application Support/Zed/settings.json
  instructions: /Users/sanath/.config/zed/AGENTS.md
  skill: /Users/sanath/.agents/skills/codebase-memory/SKILL.md (1 installed)
KiloCode:
  mcp: /Users/sanath/.config/kilo/kilo.jsonc
  instructions: /Users/sanath/.config/kilo/rules/codebase-memory-mcp.md
  agent: /Users/sanath/.config/kilo/agents/codebase-memory-scout.md
  agent: /Users/sanath/.config/kilo/agents/codebase-memory.md
  agent: /Users/sanath/.config/kilo/agents/codebase-memory-auditor.md
Pi:
  instructions: /Users/sanath/.pi/agent/AGENTS.md
  skill: /Users/sanath/.pi/agent/skills/codebase-memory/SKILL.md (1 installed)
  extension: /Users/sanath/.pi/agent/extensions/cbmem.ts
error: one or more agent configurations failed; the published/current executable was kept, and PATH/index cleanup was not attempted
error: activation stopped after one or more agent configuration or cleanup operations failed; the published/current executable was kept, and configuration changes that completed may remain. Please restart your coding-agent sessions after resolving the errors above.

Diagnostics trajectory (memory / performance / leak issues)

## Diagnostics trajectory (memory / performance / leak issues)
N/A — install-time config failure, not a memory/performance issue.

Project scale (if relevant)

N/A

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.