fix(core): ignore directories named AGENTS.md during instruction discovery - #52576

Issue for this PR

Closes #52301

Type of change

• Bug fix
• New feature
• Refactor / code improvement
• Documentation

What does this PR do?

fs.up matches any existing path, so both AGENTS.md walks also picked up directories with that name (on macOS, any folder called agents.md, e.g. a clone of a repo with that name):

• Startup instructions (config/plugin/instruction.ts): reading the directory fails with EISDIR, the project source becomes Instructions.unavailable, and every prompt fails with "Instruction initialization blocked by unavailable sources: core/instructions".
• Nested instructions after a read (tool/plugin/read.ts): the directory makes sessionInstructions.load fail, and since that failure is swallowed, every nested AGENTS.md from that walk is silently dropped, including valid ones.

fs.up gets an opt-in type: "file" | "directory" option. Both AGENTS.md walks pass type: "file", and the global AGENTS.md is skipped unless it is a regular file. Callers that legitimately match either kind (.git, which is a file in worktrees, .hg, project markers, config discovery) keep the default behaviour.

A real AGENTS.md that exists but can't be read still marks instructions unavailable, as before.

How did you verify your code works?

• Ran the dev TUI (--standalone) in a project inside $HOME with an AGENTS.md directory in its parent, a real AGENTS.md above that, an AGENTS.md directory in sub/, and a real one in sub/deeper/:
  • On v2: every prompt fails with the error above. With only read.ts on v2, reading sub/deeper/notes.txt loads no nested instructions.
  • With this PR: both startup files load, and the read loads sub/deeper/AGENTS.md.
• Checked fs.up with no type, "file" and "directory" against a real directory tree.
• bun typecheck in packages/util and packages/core; instruction, config, filesystem, git, project and read-tool tests in packages/core pass.

Screenshots / recordings

N/A

Checklist

• I have tested my changes locally
• I have not included unrelated changes in this PR