Preserve indexing size limits in freshness checks

[Widthdom]

Indexing a file above the default 4 MiB limit with an explicit larger limit could succeed, while the next ordinary freshness check reported the same readable file as both a probe failure and a deletion. Save and reuse the effective CLI/MCP size budget, preserve the budget needed by untouched files during scoped updates, and recover bounded legacy budgets from recorded file sizes without a rebuild.

Freshness comparison now consumes discovered paths even when reading fails, retaining scan-error and unverifiable evidence. Normalized content loading and its existing read bounds remain intact. CLI help and English/Japanese README, developer, and testing documentation describe the policy.

Validation

• Focused size-policy, root/shared-workspace, CLI/MCP, legacy, deletion, and failed-read tests pass on net8.0 and net9.0.
• Final regression recheck includes every initially failing test method plus size-policy, corrupt-database, dry-run, WAL snapshot, MCP recovery-marker, envelope, and watcher coverage: net8.0 passed 184; net9.0 passed 177 with 3 conditional skips; no failures.
• The initial full-suite run exercised over 12,000 tests per framework and detected preflight regressions (fixed) plus failures observed during concurrent repository indexing. All initially failing methods are covered by the successful recheck above; the entire suite was not rerun after those fixes.
• Solution build succeeds with zero warnings/errors.
• make lint passes after correcting the added test's JSON initializer formatting that failed the first CI run.
• Ordinary repository root and shared-workspace checks pass without CDIDX_MAX_FILE_BYTES.
• Changelog fragment validation passes: changelog.d/unreleased/5258.fixed.md.
• Codex adversarial review completed in two rounds. The invalid-environment fallback finding was fixed and regression-tested; final review found no blocking/actionable issues.

Fixes #5258