Two Claude Code releases shipped back-to-back this week — v2.1.205 on July 8 and v2.1.206 on July 9 — and together they fix several issues that were quietly breaking builder workflows. The most impactful: a bug where per-server MCP timeout configuration was silently ignored, forcing every long-running tool call through a 60-second wall regardless of what your config said. If you’ve been getting mysterious MCP tool failures on operations that should take two minutes, this is why.
Here’s a breakdown of what changed and what to do about each fix, verified against the official Claude Code changelog and the MCP reference docs.
The MCP 60-Second Wall Is Gone
The most consequential fix in v2.1.206: MCP servers configured via --mcp-config or .mcp.json were ignoring a per-server timeout field entirely. All MCP tool calls silently fell back to the 60-second default, regardless of what the config said. (The changelog entry itself names the field request_timeout_ms; the MCP reference docs — the authoritative source for the actual .mcp.json schema — document the real key as timeout, in milliseconds. Use timeout; request_timeout_ms is not a recognized field in .mcp.json.)
This affected any MCP integration where a tool call runs longer than a minute: large database queries, image generation pipelines, code execution sandboxes, web scraping with retries, long-context document processing. You’d set a timeout, the build would pass config validation, and then your session would fail at runtime with no explanation connecting the failure to the ignored config field.
The fix is straightforward — the field now works. How to configure it in .mcp.json, per the MCP docs:
{
"mcpServers": {
"database": {
"command": "npx",
"args": ["-y", "@myorg/db-mcp-server"],
"timeout": 300000
},
"sandbox": {
"command": "python",
"args": ["-m", "my_sandbox_server"],
"timeout": 120000
},
"fast-search": {
"command": "npx",
"args": ["-y", "@myorg/search-mcp"],
"timeout": 10000
}
}
}
One constraint to note, per the MCP docs: timeout is a hard wall-clock limit per tool call. Values below 1000 ms are ignored and fall through to the MCP_TOOL_TIMEOUT environment variable (which itself defaults to roughly 28 hours if unset) — so set per-server values to at least 1000 ms if you want them to take effect. (Older Claude Code versions, before v2.1.162, floored sub-1000ms values to a 1-second watchdog instead; that behavior no longer applies as of v2.1.206.) Separately, for HTTP/SSE/connector servers there’s a 60-second per-request timer covering only the time to the server’s first response byte — that’s the “60-second default” the changelog refers to, and setting timeout (or MCP_TOOL_TIMEOUT) to 60 seconds or higher raises it. Stdio and WebSocket servers have no such per-request timer.
/doctor Now Diagnoses Your CLAUDE.md
/doctor became a full setup checkup (with /checkup as an alias) in v2.1.205. In v2.1.206 it gained a new check: it reads your checked-in CLAUDE.md files and proposes trimming content that Claude could already derive from the codebase.
The practical issue it addresses: CLAUDE.md files tend to accumulate over time. A team documents a pattern, documents an exception, documents the exception to the exception. Eventually you have a 3,000-word instruction file loaded into context on every single turn. Most of it describes things Claude can see directly in the code.
Running /doctor (or its alias /checkup) will:
- Parse your CLAUDE.md across the project hierarchy
- Cross-reference sections against what’s observable in your file structure, imports, and conventions
- Propose specific removals with reasoning
The goal is to keep CLAUDE.md focused on what can’t be derived — organizational constraints, team conventions that don’t show up in code, environment-specific quirks, non-obvious decisions and their rationale — and strip out everything else. Leaner instruction files mean faster context loading and fewer tokens consumed on every turn.
You don’t have to accept every proposal. The command presents suggestions; you decide what to remove. It’s most useful on projects that have had multiple contributors adding instructions over several months.
EnterWorktree Confirmation
EnterWorktree now asks for explicit confirmation before entering git worktrees that live outside .claude/worktrees/ (v2.1.206). Previously the command would proceed silently.
The failure mode this prevents: you have a feature branch worktree checked out somewhere on disk for reference, and an agent command enters it and starts making changes. The worktree is real, the changes are real, but the session context was pointed at a different branch. Hard to catch, hard to roll back if you weren’t watching.
The confirmation prompt is a speed bump, not a hard block — you can still enter external worktrees, you just have to say yes explicitly. For worktrees inside .claude/worktrees/ (the managed path Claude Code creates for parallel sessions), no confirmation is required.
Auth Error Clarity
An expired login used to fail every model with the misleading error “There’s an issue with the selected model” — pointing at model configuration when the actual problem was authentication.
v2.1.206 fixes this: expired sessions now detect the auth state and prompt you to run /login directly. The old error is gone.
This was a disproportionate time sink in new-project setup and in enterprise environments where tokens expire on rotation schedules. If you’ve ever spent twenty minutes troubleshooting model picker settings when the real issue was a stale token, this is the fix.
OAuth MCP Token Refresh
MCP servers that authenticate via OAuth were requiring manual re-authentication after token refresh failures. If a refresh request failed (network blip, server-side token revocation, rate limiting), the server connection would drop and stay dropped until a human ran the auth flow again.
v2.1.206 fixes this: OAuth MCP servers no longer require manual re-authentication after a single failed token refresh. For background agent sessions that can’t interrupt for human input, this is the difference between a session completing and a session silently failing mid-run.
Background Agent Upgrades (No More Stale-Session Lag)
Before v2.1.206, a Claude Code update during an active session could cause the next background agent launch to pay a slow stale-session upgrade when you attached.
Now, per the v2.1.206 changelog: background agents upgrade to a new version in the background right after a Claude Code update installs, instead of upgrading (and stalling) when you attach.
For teams running many parallel agents or scripted agent pipelines, this removes an unpredictable latency source from session startup.
v2.1.205: Auto Mode Transcript Protection
Session transcripts record what the agent did and said. A compromised MCP tool or injected prompt could attempt to overwrite or delete transcript records — either to hide malicious actions from audit review, or to alter the apparent history in a way that confuses future sessions.
The rule makes transcript mutation a blocked auto mode action, consistent with Anthropic’s stated pattern of hardening session state that should be read-only during a run.
/commit-push-pr Respects Non-Origin Remotes
/commit-push-pr previously auto-allowed git push only to a remote named origin. v2.1.206 expands this: it now auto-allows push to the repo’s configured remote.pushDefault value, and also to the sole configured remote if only one exists — even if it’s not named origin.
This matters for repos that use an explicit remote.pushDefault (common in repos with multiple remotes: an upstream fork and a personal fork, or a CI remote alongside origin), and for self-hosted setups where the remote has a custom name. Previously you’d get a permission prompt mid-flow; now it proceeds as expected.
/code-review Quality Improvements on Opus 4.8
/code-review findings quality has been improved on claude-opus-4-8 across all effort levels — the documented effort levels are low, medium, high, xhigh, max, and ultra. No configuration change required — if you were already using Opus 4.8 for code review, the improvement applies automatically.
For reference: /code-review runs on your session’s current model. If you’ve been running reviews on Sonnet 5, the default since v2.1.197, this change doesn’t directly apply. To use Opus 4.8 for a review, switch the session model first — /model claude-opus-4-8 — then run /code-review. (There is no --model argument on the /code-review command itself; its documented syntax is /code-review [low|medium|high|xhigh|max|ultra] [--fix] [--comment] [target].)
Builder Action Items
Update immediately to pick up the MCP timeout fix:
npm install -g @anthropic-ai/claude-code@latest
claude --version # confirm you're on 2.1.206+
Add timeout to your .mcp.json for any MCP server that runs operations longer than 60 seconds (field reference). Set per-server values in milliseconds; values below 1000ms are ignored.
Run /doctor in your main project sessions. Review its proposals — trim content that Claude can infer from the code, keep content that encodes constraints, decisions, and context that isn’t visible in the file structure.
Check /commit-push-pr if your repo uses a non-origin push remote. Test it once manually after updating to confirm the new auto-allow logic covers your remote setup.
Nothing to do for the rest: the EnterWorktree confirmation, auth error clarity, OAuth token refresh, background upgrade behavior, and transcript protection all take effect automatically.
What This Update Isn’t
Neither release changes model behavior, pricing, or the default model selection (still Sonnet 5 since v2.1.197). No new major features shipped — this is an infrastructure and reliability release. The MCP timeout fix is load-bearing for any production pipeline using slow MCP tools; the rest are quality-of-life improvements that compound over time.
The official changelog has the full commit-level diff if you want to audit specific changes before deploying in a controlled environment.