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

[yzeng58]

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 <available_skills> 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