fix: regenerate invalidated modules in whole-repository-mode --update runs

[kiboook]

Fixes #99

Problem

--update --compare-to <commit> never regenerates an invalidated module
when the repo went through whole-repository documentation mode (module
clustering skipped because the repo fits in one context window). It
correctly deletes the affected module's .md, then fails every time with
IncompleteGenerationError. See #99 for the full trace of why.

Root cause

generate_module_documentation() computed the processing order only from
first_module_tree.json, which stays {} forever for whole-repo-mode
repos (only the LLM clustering path writes it) — even though
module_tree.json can have real sub-modules a prior whole-repo agent run
inserted. So the regeneration loop had nothing to iterate over for an
invalidated module.

Fix

Extracted the processing-order lookup into
DocumentationGenerator.resolve_processing_order(), which falls back to
module_tree only when first_module_tree produces an empty order. The
normal clustered-repo path is unaffected, since first_module_tree is
non-empty there and the fallback never triggers.

Testing

• Added tests/test_processing_order_fallback.py (4 unit tests, no LLM/
  network needed) covering: fallback when first_module_tree is empty,
  first_module_tree still wins when non-empty (regression safety for
  the normal path), both-empty doesn't crash, and nested children are
  still walked leaf-first through the fallback.
• Ran the new tests plus the existing tests/test_overview_structure.py
  against this change — all pass.
• End-to-end verified against the minimal repro from --update --compare-to never regenerates invalidated modules in whole-repository documentation mode (always ends in IncompleteGenerationError) #99 (tiny
  auth/payment/notification TypeScript fixture, 2 commits): before the
  fix, the run reproducibly failed with IncompleteGenerationError;
  after the fix, generate --update --compare-to <sha> succeeds, the
  changed module regenerates, the two unaffected modules are correctly
  skipped ("✓ Module docs already exists"), and the overview is rebuilt
  referencing all three.