Instruction file named `skill-instructions.instructions.md` is silently ignored

### Bug

`.github/instructions/skill-instructions.instructions.md` is silently dropped — never appears in the model's system prompt, no warning, no log. Rename to literally anything else (e.g. `skill-table.instructions.md`) with identical content and frontmatter → loads correctly.

Likely collides with the `SKILLS_INSTRUCTIONS` feature flag visible in `~/.copilot/logs/`. If that filename is reserved internally, at minimum emit a warning instead of silently swallowing user files.

### Why I care

I only needed this file in the first place because the CLI truncates the `` list (see #2314, #1130, #2416) — I have 45 skills, only ~31 show up, and the budget is a hardcoded tiny character cap. Meanwhile MCP tool schemas dump 10–100× more tokens into the same system prompt with no cap at all. It's a completely arbitrary penalty on skills.

So the workflow people are forced into — "auto-generate a skill registry file because the CLI won't load my skills properly" — is exactly the workflow that this silent filename filter breaks.

### Fix (any of)

1. Don't reserve user-space filenames; rename the internal feature.
2. Warn visibly when a matching file is found and skipped.
3. Document the reserved names.

### Affected version

1.0.30

Start by reproducing with `.github/instructions/skill-instructions.instructions.md`, then compare it with the same content under `skill-table.instructions.md`; inspect `~/.copilot/logs/` for evidence of the `SKILLS_INSTRUCTIONS` collision. Done means the reserved-name behavior is removed or a visible warning is emitted when the file is skipped, with the renamed and original files behaving as documented.

Written by the indexing model from the issue text.