[BUG]

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Title: Custom skills in ~/.claude/skills/ not surfaced in session system-reminder

Body:

Summary
Custom skills placed in ~/.claude/skills/ are functional and invocable, but are not listed in the session-start system-reminder that enumerates available skills. This means Claude cannot proactively recognize when to apply them, even though they work when explicitly invoked.

Steps to Reproduce
Create one or more custom skill .md files in ~/.claude/skills/ with proper frontmatter (name, description, type).
Start a new Claude Code session.
Ask Claude: "Do you have a custom skill for X?" where X matches the skill's description.
Claude will say no — the skill does not appear in the system-reminder skill listing.
However, invoking the skill explicitly (e.g. /my-skill or via the Skill tool by name) works correctly.
Expected Behavior
Skills in ~/.claude/skills/ should be included in the session-start system-reminder alongside Anthropic-provided skills, so Claude can proactively recognize when to apply them.

Actual Behavior
The system-reminder lists only Anthropic-provided skills. User-created skills in ~/.claude/skills/ are omitted, making them invisible to Claude unless explicitly invoked.

Additional Context
The settings.json schema has no field for manually registering custom skill paths — auto-discovery from ~/.claude/skills/ is the intended mechanism, but discovered skills are not being surfaced in session context.
This makes user-created skills significantly less useful: Claude cannot apply them without the user already knowing the skill exists and naming it explicitly, defeating the purpose of skill descriptions and trigger conditions.

What Should Happen?

Title: Custom skills in ~/.claude/skills/ not surfaced in session system-reminder

Body:

Summary
Custom skills placed in ~/.claude/skills/ are functional and invocable, but are not listed in the session-start system-reminder that enumerates available skills. This means Claude cannot proactively recognize when to apply them, even though they work when explicitly invoked.

Steps to Reproduce
Create one or more custom skill .md files in ~/.claude/skills/ with proper frontmatter (name, description, type).
Start a new Claude Code session.
Ask Claude: "Do you have a custom skill for X?" where X matches the skill's description.
Claude will say no — the skill does not appear in the system-reminder skill listing.
However, invoking the skill explicitly (e.g. /my-skill or via the Skill tool by name) works correctly.
Expected Behavior
Skills in ~/.claude/skills/ should be included in the session-start system-reminder alongside Anthropic-provided skills, so Claude can proactively recognize when to apply them.

Actual Behavior
The system-reminder lists only Anthropic-provided skills. User-created skills in ~/.claude/skills/ are omitted, making them invisible to Claude unless explicitly invoked.

Additional Context
The settings.json schema has no field for manually registering custom skill paths — auto-discovery from ~/.claude/skills/ is the intended mechanism, but discovered skills are not being surfaced in session context.
This makes user-created skills significantly less useful: Claude cannot apply them without the user already knowing the skill exists and naming it explicitly, defeating the purpose of skill descriptions and trigger conditions.

Error Messages/Logs

Title: Custom skills in ~/.claude/skills/ not surfaced in session system-reminder

Body:

Summary
Custom skills placed in ~/.claude/skills/ are functional and invocable, but are not listed in the session-start system-reminder that enumerates available skills. This means Claude cannot proactively recognize when to apply them, even though they work when explicitly invoked.

Steps to Reproduce
Create one or more custom skill .md files in ~/.claude/skills/ with proper frontmatter (name, description, type).
Start a new Claude Code session.
Ask Claude: "Do you have a custom skill for X?" where X matches the skill's description.
Claude will say no — the skill does not appear in the system-reminder skill listing.
However, invoking the skill explicitly (e.g. /my-skill or via the Skill tool by name) works correctly.
Expected Behavior
Skills in ~/.claude/skills/ should be included in the session-start system-reminder alongside Anthropic-provided skills, so Claude can proactively recognize when to apply them.

Actual Behavior
The system-reminder lists only Anthropic-provided skills. User-created skills in ~/.claude/skills/ are omitted, making them invisible to Claude unless explicitly invoked.

Additional Context
The settings.json schema has no field for manually registering custom skill paths — auto-discovery from ~/.claude/skills/ is the intended mechanism, but discovered skills are not being surfaced in session context.
This makes user-created skills significantly less useful: Claude cannot apply them without the user already knowing the skill exists and naming it explicitly, defeating the purpose of skill descriptions and trigger conditions.

Steps to Reproduce

Title: Custom skills in ~/.claude/skills/ not surfaced in session system-reminder

Body:

Summary
Custom skills placed in ~/.claude/skills/ are functional and invocable, but are not listed in the session-start system-reminder that enumerates available skills. This means Claude cannot proactively recognize when to apply them, even though they work when explicitly invoked.

Steps to Reproduce
Create one or more custom skill .md files in ~/.claude/skills/ with proper frontmatter (name, description, type).
Start a new Claude Code session.
Ask Claude: "Do you have a custom skill for X?" where X matches the skill's description.
Claude will say no — the skill does not appear in the system-reminder skill listing.
However, invoking the skill explicitly (e.g. /my-skill or via the Skill tool by name) works correctly.
Expected Behavior
Skills in ~/.claude/skills/ should be included in the session-start system-reminder alongside Anthropic-provided skills, so Claude can proactively recognize when to apply them.

Actual Behavior
The system-reminder lists only Anthropic-provided skills. User-created skills in ~/.claude/skills/ are omitted, making them invisible to Claude unless explicitly invoked.

Additional Context
The settings.json schema has no field for manually registering custom skill paths — auto-discovery from ~/.claude/skills/ is the intended mechanism, but discovered skills are not being surfaced in session context.
This makes user-created skills significantly less useful: Claude cannot apply them without the user already knowing the skill exists and naming it explicitly, defeating the purpose of skill descriptions and trigger conditions.

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

Claude Code 2.1.136

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_