Compare Directories by File Identity in tool_shadow_path

[ptr727]

Summary

tool_shadow_path (host-setup/linux/install-tools.sh) compared a PATH entry to $BIN_DIR by
literal string equality, so a doubled-slash or dot-segment spelling of $BIN_DIR (for example
$BIN_DIR// or a /./ segment) named the same directory but did not match, and the walk reported
$BIN_DIR's own managed binary as a shadow of itself. tool_note then reported it as installed
outside $BIN_DIR, and apply_tool in --upgrade mode called tool_unshadow, prompting to
remove the very binary --upgrade was about to reinstall.

Adds a file-identity (-ef) check alongside the literal comparison, gated on the PATH entry being
absolute. A local-strict-review pass on an earlier version of this fix (ungated) found that an
ungated -ef check could let a relative PATH entry that merely resolves to $BIN_DIR from the
caller's current directory short-circuit the walk and mask a real, later, absolute shadow. Gating
on is_absolute closes that without losing the identity check for the doubled-slash/dot-segment
case, and, as a side effect, also stops a directory symlinked to $BIN_DIR from being reported and
removed as a shadow through the alias.

Closes on promotion: #1865

Verification

• bash -n, shellcheck, and shfmt -d clean on the changed file.
• Two rounds of a local-strict-review pass (full-file context, adversarial), the first catching
  the relative-entry masking regression above, the second finding nothing further.
• A constructed test extracting the shipped tool_shadow_path function verifies: a doubled-slash
  spelling of $BIN_DIR reports no shadow, a dot-segment spelling reports no shadow, and a
  relative PATH entry that resolves to $BIN_DIR from the cwd does not mask a real, later,
  absolute shadow. Each case was proven to fail against the pre-fix (or, for the third case, the
  intermediate) code and pass with the final fix.

🤖 Generated with Claude Code

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
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Additional details and impacted files

@@            Coverage Diff             @@
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  Coverage           ?   55.41%           
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  Files              ?       16           
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  Misses             ?     3231           
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Flag	Coverage Δ
python-3.13	55.41% <ø> (?)

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[Copilot]

Copilot review overview

🟢 Approval recommended

The change is narrowly scoped, matches the stated failure mode, and the absolute-only gating avoids the relative-PATH masking regression.

Review effort: Lite
Findings: None

What changed in this PR

This PR fixes a false-positive “shadowing” report in tool_shadow_path by comparing PATH entries to $BIN_DIR by directory identity (inode) in addition to literal string equality, avoiding self-shadow detection when $BIN_DIR is spelled with doubled slashes or dot segments.

Changes:

• Add an absolute-only -ef identity check so $BIN_DIR// and $BIN_DIR/./... are treated as $BIN_DIR.
• Keep the early-return behavior safe by gating identity checks to absolute PATH entries, preventing relative entries from short-circuiting the scan.

File	Description
host-setup/​linux/​install-tools.sh	Updates tool_shadow_path to treat $BIN_DIR-equivalent absolute PATH entries as the same directory via -ef.

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