System prompt loader double-loads global overlay files when cwd == $HOME

[compulsivedev]

Problem

When the session working directory is $HOME, the system-prompt loader includes both the project and the global copy of each overlay file, even though they resolve to the same on-disk path. Confirmed for:

• AGENTS.md / ~/AGENTS.md
• .jcode/prompt-overlay.md / ~/.jcode/prompt-overlay.md
• .jcode/preferred-tools.md / ~/.jcode/preferred-tools.md

Result: the same content appears twice in every prompt (~2-5 KB duplicated per turn).

Repro

cd $HOME
jcode  # inspect the assembled system prompt; project + global sections are identical
readlink -f ./.jcode/preferred-tools.md ~/.jcode/preferred-tools.md   # same inode

Suggested fix

Canonicalize each candidate path (std::fs::canonicalize) and dedup before concatenation in the layer-4/5/6 loaders described in docs/SYSTEM_PROMPT_CONFIG.md.

Impact

• Wastes input tokens every turn for users who launch jcode from $HOME.
• Confuses new users about which file to edit.
• Version: v0.84.0 (57d5878).

[1jehuang]

Thanks for the precise reproduction. PR #1245 fixes the remaining duplication in prompt overlays and preferred-tools files, including symlink aliases. AGENTS.md already had canonical-path deduplication, which the two other loaders now share.

Both duplication regressions failed before the fix. All 37 prompt tests and the CLI build pass afterward, including full/split prompt assembly and character counts. The broader suite still has 11 failures, all reproduced unchanged on upstream and documented in the PR.

Commit: 1d6e2d7

The PR is not merged or released yet, so this issue remains open.

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— Jcode agent (automated triage), on behalf of @1jehuang

[1jehuang]

Linking the earlier original report, #1092, which covers the same overlay/preferred-tools duplication and character accounting. PR #1245 now references both reports. Marking this report as a duplicate for tracking only, not closing it.

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— Jcode agent (automated triage), on behalf of @1jehuang