Harden Pithos archive parsing, extraction, and block handling

[das-Abroxas]

These changes hardens pithos_lib across archive writing, parsing, reading, extraction, and append flows. It addresses multiple correctness and security issues around compression handling, path safety, external block access, malformed archive validation, directory integrity, plaintext integrity checks, header/version validation, and append-time block reuse.

What changed

• Fixed level-zero compression so archive writes honor disabled compression and preserve uncompressed payloads instead of silently transforming data.
  • Resolves [Pithos Lib] Honor disabled compression during archive writes #26
• Added archive path validation and safe extraction helpers to prevent path traversal, symlink escape, and conflicting ancestor-entry behavior.
  • Resolves [Pithos Lib] Prevent path traversal during extraction #27
• Made external block reads explicit by routing them through caller-provided block sources instead of hidden/default access paths.
  • Resolves [Pithos Lib] Make external block reads explicit and policy-controlled #28
• Hardened archive parsing with checked bounds, configurable deserialization limits, and safer length handling for malformed archives.
  • Resolves [Pithos Lib] Add checked bounds for archive parsing #29
• Improved error handling for unsupported inputs, exhausted file IDs, and invalid reader/writer inputs so they return clear errors instead of panicking or behaving unexpectedly.
  • Resolves [Pithos Lib] Handle unsupported inputs without panics #30
• Added strict directory integrity validation for markers, encoded lengths, and CRCs.
  • Resolves [Pithos Lib] Reject invalid directory markers and CRCs #31
• Enforced block/plaintext integrity checks during read and extraction so corrupted payloads fail instead of returning modified data.
  • Resolves [Pithos Lib] Validate plaintext integrity on read #32
• Rejected invalid archive headers and unsupported versions during parsing, with regression coverage for malformed header cases.
  • Resolves [Pithos Lib] Reject invalid archive headers and versions #33
• Improved append behavior by reusing existing ancestor blocks for duplicate content while detecting conflicting same-hash records.
  • Resolves [Pithos Lib] Reuse existing blocks when appending duplicate data #34

Additional changes

• Added and expanded regression coverage in pithos_lib integration tests for writer, reader, marshalling, and robustness scenarios.
• Updated dependency metadata, workspace crate versions, CI/release workflows, license files, and README badges/documentation.

Testing

• Added coverage for malformed headers, invalid archive bounds, corrupted directory metadata, plaintext/block corruption, path traversal and symlink extraction escapes, external block reads, compression level zero, and duplicate append block reuse.
• Verified the branch with the relevant pithos_lib integration tests and workspace checks.

[codecov]

Codecov Report

❌ Patch coverage is 89.62062% with 145 lines in your changes missing coverage. Please review.
✅ Project coverage is 76.60%. Comparing base (218c888) to head (6f8bd26).

Files with missing lines	Patch %	Lines
crates/pithos_lib/src/io/pithosreader.rs	79.83%	74 Missing ⚠️
crates/pithos_lib/src/model/deserialization.rs	89.58%	20 Missing ⚠️
crates/pithos_lib/src/io/extraction.rs	80.61%	19 Missing ⚠️
crates/pithos_lib/src/helpers/crypt4gh.rs	80.64%	12 Missing ⚠️
crates/pithos_lib/src/io/pithoswriter.rs	84.84%	10 Missing ⚠️
crates/pithos_lib/src/helpers/file_entry_map.rs	96.17%	6 Missing ⚠️
crates/pithos_lib/src/helpers/directory.rs	91.17%	3 Missing ⚠️
crates/pithos_lib/src/model/structs.rs	95.65%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #35      +/-   ##
==========================================
+ Coverage   69.07%   76.60%   +7.52%     
==========================================
  Files          17       19       +2     
  Lines        2985     4154    +1169     
==========================================
+ Hits         2062     3182    +1120     
- Misses        923      972      +49     

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[St4NNi]

These are quite a few long standing issues that have been fixed. LGTM!