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Convert bare boolean flags to --flag/--no-flag form with env var backing for all behavioral toggles. Add 16 new ConfigEnvVar entries for settings that benefit from project/machine-level persistence. Inverted options (old → new): --no-fetch → --fetch/--no-fetch (FetchOption, TDC_FETCH) --no-progress → --progress/--no-progress (ProgressOption, TDC_PROGRESS) Converted to dual-form with env var: --incremental/--full (+ TDC_INCREMENTAL) --prompt-credentials/--no-prompt-credentials (+ TDC_PROMPT_CREDENTIALS) --include-without-files/--exclude-without-files (+ TDC_INCLUDE_WITHOUT_FILES) --full-metadata/--brief-metadata (+ TDC_FULL_METADATA) --doc-only/--no-doc-only (+ TDC_DOC_ONLY) --auto-crawl-specs/--no-auto-crawl-specs (+ TDC_AUTO_CRAWL_SPECS) --md-yaml-frontmatter/--no-md-yaml-frontmatter (+ TDC_MD_YAML_FRONTMATTER) --include-inactive/--exclude-inactive (+ TDC_INCLUDE_INACTIVE) --skip-existing/--process-existing (+ TDC_SKIP_EXISTING) --docx-direct/--docx-convert (+ TDC_DOCX_DIRECT) --extract-media/--no-extract-media (+ TDC_EXTRACT_MEDIA) Added env vars to non-boolean extraction options: --profile (TDC_PROFILE), --figures (TDC_FIGURES), --tables (TDC_TABLES), --device (TDC_DEVICE) Destructive flags (--clear-*, --force, --delete-*, --dry-run) intentionally left without env vars to prevent accidental data loss.