[BUG] Custom agents intermittently disappear from /agents picker — files on disk, not loaded (v2.1.69)

Preflight

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report
• [x] I am using the latest version of Claude Code

What's Wrong?

Custom agent definitions in ~/.claude/agents/ intermittently fail to appear in the /agents picker. The files are confirmed present on disk — the picker simply doesn't load them.

Live repro in a single session:

1. Opened /agents picker — showed 11 agents (6 custom + 5 built-in). All 6 custom agents visible.
2. Dismissed the picker.
3. Opened /agents picker again seconds later — showed 8 agents (3 custom + 5 built-in). Three agents vanished: doc-owner, pipeline-orchestrator-5min, trading-algo-planner.
4. Confirmed all 6 .md files still present in ~/.claude/agents/ via ls -la. No file was deleted, renamed, or modified.

Directory listing at time of bug (all files present):

-rw-r--r-- 1 Cassie 197121  9577 Mar  4 16:02 1min-eod-pipeline-owner.md
-rw-r--r-- 1 Cassie 197121 11837 Mar  5 07:23 doc-owner.md
-rw-r--r-- 1 Cassie 197121 10562 Mar  5 07:42 pipeline-orchestrator-5min.md
-rw-r--r-- 1 Cassie 197121 30923 Mar  4 16:25 ram-safety-auditor.md
-rw-r--r-- 1 Cassie 197121  8754 Mar  5 07:42 trading-algo-planner.md
-rw-r--r-- 1 Cassie 197121 33010 Mar  4 16:25 wiring-auditor.md

Picker showing only 3 of 6:

User agents (C:\Users\Cassie\.claude\agents)
  1min-eod-pipeline-owner · opus · project memory
  ram-safety-auditor · opus
  wiring-auditor · opus

Missing: doc-owner, pipeline-orchestrator-5min, trading-algo-planner

What Should Happen?

All .md files in ~/.claude/agents/ should always appear in the /agents picker. File discovery should be deterministic — opening the same picker twice in the same session should show the same results.

Steps to Reproduce

1. Have 4+ custom agent .md files in ~/.claude/agents/
2. Open /agents picker — note all agents visible
3. Dismiss and reopen — some agents may be missing
4. The specific agents that disappear seem random/non-deterministic

Environment

• Claude Code Version: 2.1.69
• Platform: Windows 11
• Runtime: Node.js v24.14.0 (npm install)
• Terminal: Windows Terminal / PowerShell

Additional Context

This appears related to the session rename persistence bug (#25090) — same pattern of data on disk but the UI index/listing mechanism failing to load it. The file discovery for agents may be using a cached directory listing or file watcher that intermittently misses entries.

Also observed: an agent created in the evening didn't show up in /agents at all. The next morning it appeared without any changes. The picker's file discovery is clearly non-deterministic.