feat: centralize logging and add --verbose, --debug, --log-file flags

[rthakkar0555]

Summary

Implements structured logging across the DockSec codebase, replacing
inconsistent print() and console.print() calls with Python's standard
logging module. Adds --verbose, --debug, and --log-file CLI flags
for configurable verbosity.

Closes #52

---

Problems Fixed

• No way to increase verbosity when a scan fails silently
• Mixed output mechanisms (print, logging, rich.console) coexisting
• Subprocess stderr from Trivy/Hadolint being swallowed silently
• No --log-file option for CI/CD artifact collection

---

Changes Made

docksec/utils.py

• Added configure_logging(verbose, debug, log_file) function
• Level mapping: --debug → DEBUG, --verbose → INFO, default → WARNING
• Optional --log-file adds a FileHandler alongside StreamHandler
• Existing get_custom_logger() preserved untouched

docksec/cli.py

• Added -v/--verbose — show detailed scan progress
• Added --debug — surface raw subprocess output and tool stderr
• Added --log-file PATH — write structured logs to file
• configure_logging() called immediately after args are parsed

docksec/docker_scanner.py

• Replaced ~48 print() and console.print() calls with structured logging
• Scan progress → logger.info()
• Raw commands → logger.debug()
• subprocess stderr on failure → logger.error()
• subprocess stderr on success → logger.debug()

docksec/score_calculator.py

• Replaced all print() with logger
• Score results → logger.info()
• Score components → logger.debug()

docksec/report_generator.py

• Replaced all print() with logger
• Report saved paths → logger.info()
• Warnings (empty data) → logger.warning()
• Errors → logger.error()

tests/test_logging.py (new)

• 6 new tests covering all acceptance criteria:
  • Default level = WARNING
  • --verbose sets level = INFO
  • --debug sets level = DEBUG
  • --debug implies --verbose (DEBUG < INFO)
  • --log-file creates and writes to file
  • Zero print() calls remain in library code (AST scan)

---

Acceptance Criteria Met

• --verbose shows tool progress without debug noise
• --debug surfaces raw subprocess output and LLM timings
• --log-file PATH writes structured logs to file
• Default output unchanged (no regressions)
• Zero print() calls remain in library code
• Unit tests verify log output at different verbosity levels

---

Validation

pytest tests/ -v → 37 passed, 0 failures

(6 new logging tests + 31 existing tests, 0 regressions)

[codecov-commenter]

Codecov Report

❌ Patch coverage is 45.31250% with 105 lines in your changes missing coverage. Please review.
⚠️ Please upload report for BASE (main@7a2a48a). Learn more about missing BASE report.

Files with missing lines	Patch %	Lines
docksec/docker_scanner.py	2.63%	74 Missing ⚠️
docksec/score_calculator.py	0.00%	14 Missing ⚠️
docksec/report_generator.py	37.50%	10 Missing ⚠️
docksec/cli.py	0.00%	5 Missing ⚠️
tests/test_logging.py	97.33%	2 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #86   +/-   ##
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  Coverage        ?   42.68%           
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  Files           ?       17           
  Lines           ?     1989           
  Branches        ?        0           
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  Hits            ?      849           
  Misses          ?     1140           
  Partials        ?        0           

Flag	Coverage Δ
unittests	42.68% <45.31%> (?)

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