Not reading path-specific instruction files

[rasmusfiskerbang]

Describe the bug

Between 0.0.337 and 0.0.338 a regression happened where Gihub Copilot CLI no longer uses Path specific instructions files.

Affected version

0.0.338 Commit: 877e86a

Steps to reproduce the behavior

Create the following file structure
.github/
├── instructions/
│ └── ALL.instructions.md
└── copilot-instructions.md
README.md

With the following contents

copilot-instructions.md

Always end every answer with the tag [INSTR-OK].

ALL.instructions.md

---
applyTo: "**"
---
Always include [PATH-OK] in your answer.

Run
copilot -p "Open README.md and append a line. Include your tags." --allow-all-tools

Expected behavior

The response from copilot should include both [INSTR-OK] and [PATH-OK]

Additional context

No response

[andyfeller]

Thank you for raising up this issue, @rasmusfiskerbang! 🙇 I am going to look into custom instruction cache performance optimizations included in 0.0.338, trying to replicate this setup and step through the debugger to understand what might be going on with layering the custom instructions.

[andyfeller]

@rasmusfiskerbang : I think part of the problem you're encountering is your copilot-instructions.md file is in .github/instructions directory which is for path-specific repository instructions when it should be in .github.

Demo

$ cat .github/copilot-instructions.md                                       
Always end every answer with the tag [INSTR-OK].


$ cat .github/instructions/*.instructions.md
---
applyTo: "**"
---
Always include [PATH-OK] in your answer.


$ copilot --version
0.0.340
Commit: fac8111


$ copilot -p "Open README.md and append a line. Include your tags." --allow-all-tools
● I'll open the README.md file and append a line to it.

✓ Read README.md (102 lines)
● Now I'll append a new line to the README.md file:

✓ Edit README.md (+4 -1)
   ╭──────────────────────────────────────────────────────────────────────────────────────────────╮
   │  95                                                                                          │
   │  96   ## What is your favorite dessert?                                                      │
   │  97 - Spice cake, hands down!                                                                │
   │  97 + Spice cake, hands down!                                                                │
   │  98 +                                                                                        │
   │  99 + ---                                                                                    │
   │ 100 + *This line was added by GitHub Copilot CLI on 2025-10-15*                              │
   ╰──────────────────────────────────────────────────────────────────────────────────────────────╯
● I've successfully appended a line to the README.md file. The new line includes a timestamp and 
   indicates it was added by GitHub Copilot CLI.

   [PATH-OK] [INSTR-OK]

[rasmusfiskerbang]

That is just bad formatting on my end. copilot-instructions.md was in-fact under .github.

[andyfeller]

@rasmusfiskerbang : Thanks for the follow up. Beyond getting a little more details about your local setup (operating system, terminal, shell), I would like you to run the following and share the results here please:

gh repo clone andyfeller/copilot-cli-311
cd copilot-cli-311
copilot -p "Open README.md and append a line. Include your tags." --allow-all-tools

This is a minimal GitHub repository I recreated based on the details above using the latest build which generates the following:

$ copilot --version
0.0.342
Commit: 69ac520

$ gh repo clone andyfeller/copilot-cli-311 
Cloning into 'copilot-cli-311'...
remote: Enumerating objects: 9, done.
remote: Counting objects: 100% (9/9), done.
remote: Compressing objects: 100% (6/6), done.
remote: Total 9 (delta 0), reused 6 (delta 0), pack-reused 0 (from 0)
Receiving objects: 100% (9/9), done.

$ cd copilot-cli-311

$ copilot -p "Open README.md and append a line. Include your tags." --allow-all-tools
● I'll open the README.md file, view its contents, and append a line to it.

✓ List directory . (9 files)

✓ Read README.md (7 lines)

✓ Edit README.md (+1)
   ╭──────────────────────────────────────────────────────────────────────────────────────────────╮
   │ 1   # copilot-cli-311                                                                        │
   │ 2   Simple repository for testing github/copilot-cli#311                                     │
   │ 3 + This line was appended by GitHub Copilot CLI.                                            │
   ╰──────────────────────────────────────────────────────────────────────────────────────────────╯

● Done! I've appended a new line to README.md. [PATH-OK] [INSTR-OK]


Total usage est:       1 Premium request
Total duration (API):  21.2s
Total duration (wall): 23.2s
Total code changes:    1 lines added, 0 lines removed
Usage by model:
    claude-sonnet-4.5    0 input, 0 output, 0 cache read, 0 cache write (Est. 0 Premium requests)

[andyfeller]

@rasmusfiskerbang : I'm genuinely unable to reproduce this problem as shown in #311 (comment) assuming we're talking about the custom instructions in .github directory.

I'd like to continue working with you on a reproducible situation that we can put under debug and figure out if there is some race condition contributing to your situation. In the mean time, I'm going to close this issue, which we can reopen as this develops.