copilot-instructions.md are not used in a multi-root worksapce

[krubenok]

Type: Bug

open a multi-root workspace with several directories, instructions contained at .github/copilot-instructions.md in one of the repos is never used despit trying both absolute and relative paths in the chat.instructionsFilesLocations settings of the .code-workspace file.

Adding an absolute path to the .github/instructions directory to the .code-workspace file setting as above does include instructions when required by the applyTo pattern.

code-workspace file

relevant snippets

{
    "folders": [
        {
            "path": ".."
        },
        {
            "path": "../../outlook-web-wiki"
        }
    ],
	"... some other stuff....",
	"github.copilot.chat.codeGeneration.useInstructionFiles": true,
    "chat.agent.maxRequests": 1000,
    "chat.instructionsFilesLocations": {
        "/workspaces/client-web/.github/instructions": true,
        "/workspaces/client-web/mcp-server/copilot-agent/instructions": true
    },
    "chat.modeFilesLocations": {
        "/workspaces/client-web/mcp-server/copilot-agent/chatmodes": true
    }
}

Extension version: 0.31.2025090201
VS Code version: Code - Insiders 1.104.0-insider (a2b1ec5, 2025-09-02T15:56:07.546Z)
OS version: Darwin arm64 25.0.0
Modes:
Remote OS version: Linux x64 6.8.0-1030-azure

System Info

Item	Value
CPUs	Apple M3 Max (16 x 2400)
GPU Status	2d_canvas: enabled direct_rendering_display_compositor: disabled_off_ok gpu_compositing: enabled multiple_raster_threads: enabled_on opengl: enabled_on rasterization: enabled raw_draw: disabled_off_ok skia_graphite: enabled_on trees_in_viz: disabled_off video_decode: enabled video_encode: enabled webgl: enabled webgl2: enabled webgpu: enabled webnn: disabled_off
Load (avg)	3, 3, 4
Memory (System)	64.00GB (1.63GB free)
Process Argv	--crash-reporter-id 80cc1fb8-9d9f-4502-9401-54c11b320af9
Screen Reader	no
VM	0%

Item	Value
Remote	Codespaces: opulent train
OS	Linux x64 6.8.0-1030-azure
CPUs	AMD EPYC 7763 64-Core Processor (32 x 0)
Memory (System)	125.79GB (117.52GB free)
VM	0%

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copilot_t_ci:31333650
g012b348:31231168
pythoneinst12:31251391
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996jf627:31264550
pythonrdcb7:31268811
usemplatestapi:31297334
747dc170:31275146
6518g693:31302842
0g1h6703:31329154
agentisdefault:31374427
6abeh943:31336334
envsactivate1:31349248
0927b901:31340060
custommodelcf:31371783
editstats-enabled:31346256
gendocstringt:31371829
gemagent1cf:31368470
cloudbuttont:31366566
aihoversummaries_f:31371859
todos-1:31366868
codex-prompt:31370221
search_len2:31376507
multireplacestring:31375832
nb255704_tf:31377673
3efgi100_wstrepl:31374188
nes-auto-20:31375598
test_plugin_ver_c:31378989

[aeschli]

Fixed by #264926