fix: treat missing log marker outputs as unprocessed

[atsyplenkov]

Summary

• make non-overwrite runs block only on <output>/<pdf_stem>/log.jsonl; when marker is missing, refresh managed artifacts and continue
• add regression coverage for stale index.md/figures/tables without log marker, plus ordering checks around env lookup
• align CLI help, README, and changelog with marker-based semantics

Test Plan

• cargo test
• cargo test --test cli_existing_output
• cargo test --features internal-testing --test core_internal
• env -u ZAI_API_KEY cargo run -- --input /home/ats/Projects/watemsedem_review/data/pdf/chen_2022_linkages_between_soil_erosion_and_long-term_changes_of_landscape_pattern_in_a_small_watershed_on_the.pdf --output /home/ats/Projects/watemsedem_review/data/md --normalize-tables --env-file /tmp/paperdown-missing.env

[codecov-commenter]

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Codecov Report

❌ Patch coverage is 97.81022% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 86.19%. Comparing base (3745eab) to head (6ebda1f).

Files with missing lines	Patch %	Lines
src/main.rs	97.82%	2 Missing ⚠️
src/core/output.rs	97.29%	1 Missing ⚠️
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Additional details and impacted files

@@            Coverage Diff             @@
##             main      #14      +/-   ##
==========================================
+ Coverage   85.26%   86.19%   +0.93%     
==========================================
  Files           9        9              
  Lines        1751     1855     +104     
==========================================
+ Hits         1493     1599     +106     
+ Misses        258      256       -2     

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