fix: ls -R hierarchy + tracking baseline + incompatible flags (#714, #561)

[pszymkowiak]

Closes #714, Closes #561

Changes

1. ls -R hierarchy (rtk ls -R flattens recursive output and loses hierarchy context #714): recursive output now shows directory structure with indentation
2. Tracking baseline (fix: ls tracking baseline should compare against ls not ls -la #561): savings compared against plain ls (not ls -la)
3. Incompatible flags: -1, -d, -F, -i, -p passthrough to raw ls

Before/After

BEFORE (flat):               AFTER (hierarchy):
empty-dir/                    readme.md  6B
group-a/                      empty-dir:
group-b/                      group-a:
nested/                         details.md  8B
readme.md  6B                   overview.md  11B
details.md  8B                group-b:
overview.md  11B                examples.md  9B
examples.md  9B                 overview.md  11B
overview.md  11B                nested:
notes.md  6B                      notes.md  6B

LLM comprehension test

20 ls variants tested with llama3.1:8b, phi4:14b, Claude — 100% comprehension on hierarchy.

• 1114 tests passing
• All 20 ls variants working (basic, sort, recursive, edge cases)
• LLMs correctly identify file locations in recursive output

[pszymkowiak]

[w] wshm · Automated triage by AI

📊 Automated PR Analysis

🐛 Type	bug-fix
🟡 Risk	medium

Summary

Fixes recursive ls output to display directory hierarchy with indentation instead of flat listing, changes the tracking baseline to compare against plain ls rather than ls -la, and adds passthrough for flags incompatible with the -l parser (-1, -d, -F, -C, -m, -x, -i, -p).

Review Checklist

• Tests present
• Breaking change
• Docs updated

Linked issues: #714, #561

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Analyzed automatically by wshm · This is an automated analysis, not a human review.

[aeppling]

Hey

We are cleaning up the codebase and improving the project structure for better onboarding. As part of this effort, PR #826 reorganizes src/ from a flat layout into subfolders.

No logic changes — only file moves and import path updates.

What you need to do

Rebase your branch on develop when receiving this comment:

git fetch origin && git rebase origin/develop

Git detects renames automatically. If you get import conflicts, update the paths:

use crate::git;        // now: use crate::cmds::git::git;
use crate::tracking;   // now: use crate::core::tracking;
use crate::config;     // now: use crate::core::config;
use crate::init;       // now: use crate::hooks::init;
use crate::gain;       // now: use crate::analytics::gain;

Need help rebasing? Tag @aeppling

[mgierok]

I I believe this is a very necessary fix. Codex, in particular, has significant difficulties working without it, which in practice leads to increased token usage.

[pszymkowiak]

Closing — superseded by #1251.

This PR was based on the pre-refacto src/ls.rs and could not be rebased cleanly after the module moved to src/cmds/system/ls.rs with the new runner::run_filtered architecture (refacto #904). #1251 ports the fix to the current codebase with the same scope (recursive hierarchy + incompatible flags passthrough).