Project-level skills disappear from available list mid-session

Bug Description

Project-level skills (defined in <project>/.claude/skills/) are correctly discovered and available at session start, but silently disappear from the available skills list mid-session. Attempting to invoke them after they disappear returns "Unknown skill."

Steps to Reproduce

1. Create a project-level skill in .claude/skills/<name>/SKILL.md with valid frontmatter
2. Start a new Claude Code session in the project directory
3. Verify the skill appears in the system reminder's available skills list — it does
4. Continue working in the session (several tool calls, possibly triggering context compression)
5. Observe that the skill is no longer listed in subsequent system reminders
6. Attempting Skill("name") returns: Unknown skill: name

Expected Behavior

Project-level skills should remain available for the entire session duration, surviving context compression and skill list refreshes.

Actual Behavior

• Session start: skill is listed and invocable ✅
• Mid-session: skill silently drops from the available list ❌
• Invoking it returns "Unknown skill" ❌

Environment

• Claude Code CLI (Opus 4.6)
• Linux (Fedora 42)
• Global ~/.claude/skills/ contains 3 skills (via GNU Stow symlinks)
• Project .claude/skills/ contains 2 skills (regular files, committed to git)
• Global ~/.claude/settings.json is symlinked via GNU Stow (no skill filtering keys)
• Project .claude/settings.json has hooks only (no skill filtering)

Notes

• Global skills (~/.claude/skills/) remain available throughout — only project-level skills disappear
• Project-level agents (.claude/agents/) remain available throughout — only skills are affected
• The skill files themselves are unchanged on disk when the disappearance occurs
• No errors or warnings are logged