bug: VSCode extension duplicates project skills in context when multiple working directories are configured

Summary

The VSCode extension duplicates project skills in the LLM system prompt when multiple working directories (multi-root workspace) are configured. Each skill from .claude/skills/ in the primary project directory is injected once per working directory instead of once total. For example, with 3 workspace folders and 13 custom skills, the system prompt contains 39 skill entries (13 x 3) instead of 13 — tripling the token cost for skills from ~370 to ~1,100 tokens. The /context command confirms each skill listed 3 times with source "Project".

Motivation

Unnecessary token consumption in the system prompt. While the per-session impact is small (~730 wasted tokens with 13 skills x 3 directories), it adds up across sessions and could become more significant with larger skill sets or more working directories. It also makes the /context output confusing as it suggests misconfiguration.

Out of Scope

• Skills loaded from different projects that happen to share the same name (legitimate separate skills)
• Deduplication of built-in/system skills

Dependencies / Blockers

N/A

Specification

Environment: Claude Code VSCode Extension (native extension mode), Windows 11, claude-opus-4-6

Steps to reproduce:

1. Open a VSCode workspace with multiple folders (e.g., 3 projects in a multi-root workspace)
2. Only the primary project has .claude/skills/ with custom SKILL.md files
3. The additional working directories have no .claude/skills/ directory
4. Start a Claude Code session
5. Run /context to inspect token usage

Expected: Each skill appears once in the context
Actual: Each skill appears N times (where N = number of working directories)

Evidence from /context output:

### Skills

| Skill | Source | Tokens |
|-------|--------|--------|
| brainstorming | Project | 53 |
| brand-guidelines | Project | 26 |
| debug | Project | 31 |
| ...                              |
| brainstorming | Project | 53 |
| brand-guidelines | Project | 26 |
| debug | Project | 31 |
| ...                              |
| brainstorming | Project | 53 |
| brand-guidelines | Project | 26 |
| debug | Project | 31 |
| ...                              |

Each skill block is identical and repeats once per working directory.

Suggested Doc Updates

N/A — this is a runtime behavior fix.

Suggested Files

| Path | Reason |
| - | - |
| Skill loading / registration logic in the VSCode extension | Deduplication needed when iterating over working directories |

Acceptance Criteria

• [ ] Skills from the primary project are loaded exactly once regardless of how many additional working directories are configured
• [ ] /context output shows each skill only once
• [ ] No regression when skills exist in multiple working directories (each unique skill still loads correctly)