Why I Killed My 4th Claude Code Instance — Lessons from Multi-Agent Indie Dev

#claude #buildinpublic #webdev #productivity

Why I Killed My 4th Claude Code Instance

The Setup

I'm building a Flutter Web + Supabase app called "Jibun Inc." — an AI life-management hub that absorbs the features of 21 competitors (Notion, Evernote, MoneyForward, Slack, etc.) into one. The AI University module just passed 66 providers today.

My dev loop runs four Claude Code instances in parallel:

VSCode instance → lib/ (Flutter UI) and supabase/functions/
Windows Desktop instance → docs/ and supabase/migrations/
PowerShell instance → .github/workflows/ and CI/CD
Web instance (claude.ai/code) → blog translation and PR review via GitHub MCP

Today I shut down the Web instance. Here's why, and what I learned about keeping a multi-agent workflow stable.

What Broke

Inside a single Web-instance session I hit three different failures:

GitHub MCP dropped the connection three times.
The v2.1.110 fix for MCP tool calls hanging when server connection drops is apparently not deployed to the claude.ai/code runtime. Each reconnect cost a few minutes.
Stream idle timeout — partial response received when I ran WebFetch in parallel with file edits. The response was cut off mid-flight and the session couldn't recover.
A false "file not found" read on docs/INSTANCE_CONFIG.md, which triggered a new-file creation attempt — a violation of file-ownership boundaries, because that file belongs to the PowerShell instance. The underlying cause was a dropped MCP call, but the agent didn't know.

Any one of these would be survivable. Hitting all three in one session makes the workflow unshippable.

The Fix: Back to Three

I did a 5-file cleanup to remove every reference to the Web instance:

docs/MULTI_INSTANCE_COORDINATION.md  — title 4→3, drop Web row
docs/INSTANCE_CONFIG.md              — delete Web constraints/prompt/role
docs/README.md                       — 4→3 instances
CLAUDE.md                            — strip Web mentions from Rules 14/21/22
.github/COMPRESSED_PROMPT_V3.md      — header 4→3, scope table

git show 95c385a4 --stat reported 149 deletions / 29 additions. The Web instance had crept into more places than I expected.

Redistributing the Work

Old Web-instance duty	New owner
`docs/research/` and `docs/blog-drafts/`	Windows Desktop (already owns `docs/`)
GitHub MCP PRs and issue triage	PowerShell (`gh` CLI works there)
Opus 4.7 architecture reviews	Windows Desktop / PowerShell
Blog English translation	PowerShell (yes, even this post's EN version)

Just clarifying who can write what collapsed most of my merge conflicts.

Gotchas

Cross-instance write permission

docs/INSTANCE_CONFIG.md is owned by PowerShell, but the decision to retire the Web instance came from the Windows Desktop session. I built a small escape hatch for exactly this case: drop a note in docs/cross-instance-prs/YYYYMMDD_<topic>.md and let the owning instance approve it next session.

When it's urgent, I edit the file directly and tag the commit message with [cross-instance: PowerShell approval required].

Keeping forbidden regions forbidden

Windows Desktop's write scope is docs/ (minus DESIGN.md) plus supabase/migrations/. Today's change also touched CLAUDE.md and .github/COMPRESSED_PROMPT_V3.md, which are explicitly marked as shared territory. The permission table let me make that call instantly instead of stalling.

Don't accidentally commit an unrelated change

My working tree had uncommitted edits to lib/pages/admin/quota_dashboard_page.dart from a parallel instance. I avoided git add -A and listed each file explicitly:

git add \
  docs/MULTI_INSTANCE_COORDINATION.md \
  docs/INSTANCE_CONFIG.md \
  docs/README.md \
  CLAUDE.md \
  .github/COMPRESSED_PROMPT_V3.md

Takeaways

The Web instance of Claude Code is not production-grade for an automated dev pipeline today. I'll reconsider once MCP stability matches the local runtime.
Document the permission boundaries of every agent up front. Undoing a deployment is fast when you know exactly what to grep.
Commit only what you meant to change. Name your files; don't trust git add -A inside a multi-agent repo.

Next post: how I rebuilt the blog-draft pipeline in GitHub Actions so posts stop going silent.

Building in public: https://my-web-app-b67f4.web.app/