`.github/hooks/*.json` are not loaded in non-interactive (`copilot -p`) mode, but load correctly in interactive mode

[torumakabe]

Describe the bug

Repository-level hook files (.github/hooks/*.json and inline hooks in .github/copilot/settings.json) are not loaded when Copilot CLI is started in non-interactive print mode (copilot -p "..."). The exact same hook configuration loads and fires correctly when the CLI is started in interactive mode (TTY).

User-level hooks (~/.copilot/hooks/*.json and inline hooks in ~/.copilot/settings.json) load and fire correctly in both modes, as do plugin-defined hooks.

This is not documented as a -p-specific limitation in the Hooks reference, which lists .github/hooks/*.json as a supported source.

Affected version

• CLI version: 1.0.49-1 (macOS, Darwin 24.x)
• Reproducible across two independent repositories
• Behavior unchanged with --log-level all

Steps to reproduce

1. Create .github/hooks/pre-tool-use.json in a repo:

   {
     "version": 1,
     "hooks": {
       "preToolUse": [
         {
           "type": "command",
           "bash": "echo \"HOOK FIRED at $(date)\" >> /tmp/copilot-hook-log.txt; echo '{\"permissionDecision\":\"allow\"}'",
           "timeoutSec": 10
         }
       ]
     }
   }

2. Run non-interactive:

   copilot -p "view README.md" --allow-all-tools

   → /tmp/copilot-hook-log.txt is not created. ~/.copilot/logs/process-*.log shows only Loaded N hook(s) from N plugin(s) (user-level hooks and plugin hooks). No discovery message for .github/hooks/ appears.

3. Run interactive (same directory, same hook file):

   copilot --allow-all-tools
   # Then type: view README.md

   → /tmp/copilot-hook-log.txt is created with HOOK FIRED at .... ~/.copilot/logs/process-*.log shows the .github/hooks/ discovery and load messages.

Variations tested (all reproduce the bug in -p mode)

Variation	Result in -p
Default invocation (copilot -p "...")	❌ Repo hook not loaded
Clean env (env -i HOME=$HOME PATH=$PATH copilot -p "...")	❌ Repo hook not loaded
Absolute path to repo as cwd	❌ Repo hook not loaded
--log-level all	❌ Repo hook not loaded (logs confirm absence of discovery)
preToolUse event	❌ Not loaded
permissionRequest event	❌ Not loaded
.github/copilot/settings.json with inline hooks	❌ Not loaded
Same config via ~/.copilot/hooks/*.json (user-level)	✅ Loaded and fired
Same config via ~/.copilot/settings.json (user-level inline)	✅ Loaded and fired
Plugin-defined hooks.json	✅ Loaded and fired

Expected behavior

.github/hooks/*.json and .github/copilot/settings.json should be loaded in both interactive and non-interactive (-p) modes, matching the official documentation. CI / automation pipelines that use copilot -p "..." rely on repository-level hooks for security policy enforcement, audit logging, and tool gating.

Actual behavior

Repository-level hooks are silently ignored in -p mode. There is no warning, error, or log message indicating that the hook configuration was found but skipped.

Security implication

Teams using .github/hooks/ to enforce security policies (e.g., blocking access to local credential caches, secret patterns; gating destructive shell commands; logging tool calls for audit) lose all of that protection when the CLI is invoked non-interactively. This is especially impactful for:

• GitHub Actions workflows that run copilot -p "..."
• Cron jobs and scheduled automation
• CI hook test workflows (the hook tests themselves may pass via interactive simulation while the actual production -p calls bypass hooks)

The asymmetry between interactive and -p modes is also a footgun — users testing hooks interactively will see them work, then have them silently fail when deployed.

Workaround

Move all security-critical hooks to user-level (~/.copilot/hooks/*.json or ~/.copilot/settings.json) and distribute via dotfiles or setup scripts. Use --deny-tool 'kind(...)' on the CLI invocation for guaranteed enforcement, since --deny-tool is not affected by the hook loading bug.

Additional context

• Confirmed with logging-only hooks (return {"permissionDecision":"allow"}) and policy hooks (return {"permissionDecision":"deny"}).
• The process-*.log for a non-interactive run contains plugin and user-level hook discovery messages but never any .github/hooks/ line.
• Sub-agent hook firing (a related issue preToolUse hooks are not enforced in subagents #2392) was correctly fixed in v1.0.49-0 — this -p-mode loading bug is a separate, narrower problem on the discovery/configuration-load path, not on the runtime dispatch.

Related

• preToolUse hooks are not enforced in subagents #2392 — preToolUse hooks are not enforced in subagents (CLOSED — completed in v1.0.49-0, ✅ verified working in v1.0.49-1)
• sessionStart hook in .github/hooks/ does not fire in Copilot CLI (v0.0.420) #1730 — sessionStart hook in .github/hooks/ does not fire (OPEN; the -p loading bug reported here may be a more general manifestation of the same code path)