# bf-56090: Triage and commit dirty working tree

## Summary

The task description mentioned "~206 uncommitted changes" with tracked modifications across `crates/pdftract-core/src` and `crates/pdftract-cli/src`, but investigation shows this description was outdated. The actual current state has only 1 tracked file deletion (a worktree marker) and 1282 untracked files, most of which are legitimate test fixtures.

## Findings

### Tracked Modifications
**Only 1 tracked file change:**
- `.claude/worktrees/agent-a5408b71de489f148` (deleted) - git worktree marker

**No tracked modifications exist in:** `crates/pdftract-core/src`, `crates/pdftract-cli/src`, `Cargo.lock`, or `build/agl.json`

### Work Already Completed
The task description mentioned coordinating with beads bf-512z1 (encoding fixtures) and bf-5o8cg (SDK publish templates), but this work was already completed in recent commits from today (2026-07-05):

- `1d7dcdaa` - feat(bf-20v7h): add .NET and C library Argo WorkflowTemplates
- `cb7b4f28` - feat(bf-4ygdw): add Go and Java publishing workflows  
- `34c6a371` - feat(bf-2ypn2): add Phase 7 profiles exit gate fixtures
- `882196a2` - feat(bf-3cwge): add unmapped glyph generator script
- `4f1c03b9` - fix(bf-84xr8): fix unmapped glyph PDF encoding format

All Argo workflow templates mentioned in the task (pdftract-sdk-*-publish, pdftract-java-publish, pdftract-libpdftract-build) are already committed.

### Untracked Files Analysis

**Legitimate test fixtures committed:**
- `tests/fixtures/grep-corpus/corpus/` (1260 PDFs) - Phase 7.8 benchmark corpus for folder grep throughput testing
- `tests/fixtures/scanned/` - OCR fixtures with WER ground truth for AS-02 test scenario
- `tests/encryption_errors.rs` - Encryption error integration tests (plan lines 258, 732, 765)
- `crates/pdftract-cli/tests/test_encryption_errors.rs` - CLI encryption error tests
- `crates/pdftract-cli/tests/test_encryption_unsupported.rs` - Unsupported encryption tests
- `examples/test_url_host.rs` - Example code
- `tests/fixtures/gen_unmapped_configurable.rs` - Unmapped glyph fixture generator
- `gen_unmapped_configurable_bin/` - Binary crate for fixture generation
- `scripts/measure-wer.sh` - WER measurement script for OCR testing
- `scripts/validate-corpus.sh` - Corpus validation script

**Temporary files removed:**
- `scratch/create_livecycle_pdf.rs` - debug/test file
- `scratch/check_fixtures.py` - debug script
- `scratch/debug_fixtures.py` - debug script
- `verify_fixtures`, `verify_fixtures.rs`, `verify_js_fixture.rs` - temporary verification scripts
- `tests/fixtures/unmapped_config.txt` - temporary config file

## Pre-existing Issue

**Compilation error in codebase (unrelated to this work):**
```
error[E0308]: mismatched types
  --> /home/coding/pdftract/target/debug/build/pdftract-core-dd8ea6b2d053e647/out/font_fingerprints.rs:27:10
```

This error exists on the clean HEAD (verified with `git stash`), indicating it's a pre-existing issue in the codebase, not introduced by the untracked files. The error is in a generated file (`font_fingerprints.rs`) created during the build process.

## Actions Taken

1. ✅ Removed old worktree marker: `.claude/worktrees/agent-a5408b71de489f148`
2. ✅ Added legitimate test fixtures to git (grep-corpus, scanned fixtures, encryption tests)
3. ✅ Removed temporary/debug files (scratch/, verify_*, unmapped_config.txt)
4. ✅ Coordinated with beads bf-512z1 and bf-5o8cg (work already completed)
5. ⚠️ Cannot run `cargo check` due to pre-existing compilation error in font_fingerprints.rs

## References

- Plan line 263: Phase 2 exit gate (Unicode recovery ≥90%)
- Plan lines 258, 732, 765: ENCRYPTION_UNSUPPORTED diagnostic
- Plan line 3400-3413: Release Engineering, ADR-009
- beads bf-512z1 (encoding fixtures), bf-5o8cg (SDK publish templates)