Bootstrap does not enable GitHub Issues on forked repos

[alanzabihi]

Context

Branch: hybrid-agent-cli (PR #118)
Wave: 1 (no dependencies, safe to fix in parallel with other wave-1 issues)
Found by: polytest run 20260423-003528, hit on 3 repos independently (es-abstract, ini, qs)

Bug

polyresearch bootstrap succeeds on a forked repo but leaves GitHub Issues disabled. Since GitHub forks have Issues disabled by default, every subsequent command (audit, lead, status) fails with:

Error: GitHub CLI command failed: the 'samadin-123/es-abstract' repository has disabled issues
   Hint: Enable Issues in your repository settings: gh api repos/OWNER/REPO --method PATCH -f has_issues=true

The entire polyresearch protocol depends on Issues (theses, claims, releases, attempts are all issue comments). A fork with Issues disabled is completely unusable.

Fix

In the bootstrap command, after cloning/forking, check if Issues are enabled and enable them if not:

gh api repos/OWNER/REPO --method PATCH -f has_issues=true

This is a single API call. Do it unconditionally during bootstrap — it's a no-op if Issues are already enabled.

Repos affected

• samadin-123/es-abstract (forked from ljharb/es-abstract)
• alanzabihi/qs (forked from ljharb/qs)
• alanzabihi/ini (forked from npm/ini)

Relevant files

• cli/src/commands/bootstrap.rs
• cli/src/github.rs (the error originates at line 1009)

Severity

High — blocks all protocol operations on any forked repo.

[alanzabihi]

Still occurring on hybrid-agent-cli (commit 305dc9e)

Polytest run 20260423-133619 found 3 new instances on fresh repos:

• langchainjs (forked from langchain-ai/langchainjs)
• tiktoken (forked from openai/tiktoken)
• js-beautify (forked from beautify-web/js-beautify)

Bootstrap completes but Issues remain disabled. All subsequent commands fail.