Keep structured command output clean

[JordanNoone]

Summary

• add --json to file conversion, project publication, and project upload
• preserve the existing human-readable default: table-mode status messages remain on stdout
• keep stdout machine-readable for --json, --format=json, and --format=yaml by sending status messages to stderr
• reject ambiguous combinations of --json with --format

Tests

• cargo fmt --all -- --check
• cargo check --all-targets
• cargo clippy --all-targets -- -D warnings
• cargo test cmd_project::tests
• cargo test cmd_file::test
• verified help output for all three commands and the --json/--format conflict

The token-backed conversion integration test now covers both the unchanged default output and the new --json behavior in CI.

Closes #1757

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 65.97%. Comparing base (8d886cc) to head (e74fc2a).
⚠️ Report is 7 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1831   +/-   ##
=======================================
  Coverage   65.97%   65.97%           
=======================================
  Files          43       43           
  Lines        8434     8436    +2     
=======================================
+ Hits         5564     5566    +2     
  Misses       2870     2870           

Flag	Coverage Δ
unittests	65.97% <100.00%> (+<0.01%)	⬆️

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[jessfraz]

can you explain why, this isnt traditional for a cli, in most cases youd want something human readable in stdout unless the user gives a --json flag for only json output

[JordanNoone]

Updated based on this feedback: the affected commands now have an explicit --json flag. Without it, the default/table behavior is preserved and human-readable status stays on stdout. With --json, stdout contains only JSON and status moves to stderr. Existing explicit --format=json and --format=yaml remain machine-clean, and --json conflicts with --format to avoid ambiguity.