fix: preserve DeepSeek thinking events

Merge pull request #14 from towardsai/fix/deepseek-default-leftovers

docs(evals): F38 numeric refinements from the repricing verification writeup

docs: staleness sweep for core and pipeline docs

docs(evals): findings F35-F38, battery v2 confound corrections, staleness fixes

feat(evals): paired lockstep runner, lossless subagent grading, deprecated-battery guard

feat(experiments): DeepSeek stage-1 compaction arms + prefix-preserving summarization

chore: ignore the local full_stack_course working dir (private course content)

fix(chat): keep one thread on one provider, drop the unselectable Gemini

test(chat): cover effective_tool_names for the default DeepSeek model

fix(tests): join live text deltas without separators, test a selectable Anthropic model

docs: describe the DeepSeek default + Gemini 2.5 fallback accurately

fix(retrieval): store the BM25 index as gzipped JSON instead of pickle (#13)

Format DeepSeek default tests

Use direct DeepSeek as default model

Use OpenRouter DeepSeek with Gemini fallback

chore(versions): capture 2026-07-06 docs refresh, purge retired openai_cookbooks

fix(versions): llms.txt sources get version=null, not a Last-Modified date

fix(pipeline): single-source runs rebuild all_sources_data.jsonl safely

fix(evals): check_triggers evaluates every run before aggregating

fix(evals): never judge faithfulness on silently truncated evidence

fix(pipeline): make upload_data_to_hf report failure honestly

fix(registry): retire sources from every registry dict, not just the first

fix(data-hygiene): gitignore the retire workflow's .bak backups

fix(public-bundle): fail closed on non-allowlisted raw and wiki content

fix(pipeline): re-embed chunks whose content changed in place

fix(pipeline): stop incremental context runs gutting updated sources

fix(frontend): number citations whose labels contain balanced brackets

fix(frontend): source info popover tracks scroll

fix(activity): repeated Gemini search queries start a fresh cycle

fix(graphrag): query-relevant community reports, rerank floor parity

fix(retrieval): budget skip, standard RRF, fail-fast collection load

fix(config): restore default dotenv precedence (shell wins over .env)

fix(config): honor AI_TUTOR_KB_DIR for every KB path

fix(citations): keep labels of links with balanced brackets

perf(citations): cache the KB manifest indexes

fix(api): close request-size gaps in body and history caps

fix(api): emit stream error frame after cleanup parts

chore(frontend): TypeScript 6.0.3 + lucide-react 1.23.0

chore(deps): refresh backend lock + frontend deps; Node 22 builder

fix(citations): handle malformed links; count only consulted docs in activity (#12)

Public docs-only bundle: allowlist filtering, leak audit, kb.tar.gz cold start (#11)

wip: eval harness + public docs bundle; relocate eval docs into evals/ (#10)

chore: add LICENSE, security policy, and issue/PR templates (#9)

feat(registry): rename agentic_ai_engineering label to "Agent Engineering: Building Multi-Agent Systems"

fix(citations): drop code-block URLs from chips; default URL reading off

feat(kb): register guardrails and serving topic pages in wiki scaffolder

Add 10-Hour LLM Primer course as a new KB source

feat(prompts): add course content reproduction policy and related tests

chore: remove outdated context engineering documentation files