Filter hidden directories relative to every include root

[willemkokke]

Fixes #4526. One of the two PRs replacing #4402, split per review feedback — the other is #4527 (crates/pyrefly_util/src/globs.rs). The two touch disjoint files and can land in either order.

Problem. Follow-up to #2402. The HiddenDirFilter::RelativeTo allowance carried only import_root, so for a src-layout project (import_root = <project>/src) an include outside it — tests/check.py — prefix-matched no root and fell back to absolute-path component checking, where a checkout under a hidden directory (~/.codex/worktrees/…, .claude/worktrees/…) has every ancestor chain hidden and the include was silently dropped. The root list was also derived from use_ignore_files, so --use-ignore-files=false degraded the filter to HiddenDirFilter::All and hid the project entirely.

Approach. Build the allowance from every include root plus the import root, independent of use_ignore_files.

Why it works. has_hidden_component checks components relative to the most specific matching root, so listing every root the project actually declares means each of the project's files is judged relative to a root it lives under — hidden ancestors above the project stop mattering, while hidden directories inside it (src/.venv/…) are still excluded. And the allowance describes where the project lives, which has nothing to do with whether ignore files are consulted, so disabling one mechanism no longer hardens the other.

Tests. New test_hidden_dir_filter_is_relative_to_every_include_root covers a src-layout project under .claude/worktrees/… with a tests/ include, in both use_ignore_files states, and asserts src/.venv/… is still excluded; it fails on main (tests/check.py not covered) and passes with the fix. The existing test_get_filtered_globs_coverage_scope expectation is updated to the new RelativeTo construction. cargo test -p pyrefly_config passes.

[meta-codesync]

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