docs: sync README files with latest repo state

[yyiilluu]

Summary

• Syncs model-facing code-map READMEs with the current Reflexio package/server layout, following how_to_write_readme.md.
• Removes stale references to deleted server scripts, legacy LLM client files, profile_updater.py, and nonexistent reflexio/db / reflexio/data areas.
• Updates navigation for lib/reflexio_lib.py, LLM embedding/provider/rerank modules, and the current async extraction files.

Repositories/submodules reviewed

• Parent: yyiilluu/reflexio-enterprise
• Submodule: ReflexioAI/reflexio

README files updated

• reflexio/README.md
• reflexio/server/README.md
• reflexio/server/services/README.md

Validation

• git diff --check
• Targeted stale-token check for removed/nonexistent paths mentioned above

Notes/Risks

• open_source/reflexio/README.md was intentionally not restructured because it is the user-facing public README and is excluded by the parent repository README policy.
• Parent repository submodule pointer was not committed; this PR is scoped to the submodule docs only.

Summary by CodeRabbit

• Documentation
  • Updated comprehensive architecture documentation to reflect revised component structure and organizational paths
  • Enhanced documentation clarity for library, server, and service modules with clarified relationships
  • Refined service pipeline flow descriptions and component dependency documentation
  • Removed outdated configuration sections from service documentation

[coderabbitai]

📝 Walkthrough

Walkthrough

Three README files are updated to reflect the current component structure. reflexio/README.md adds a lib section, refreshes server paths and the component relationship diagram, updates storage descriptions, and replaces the data/ section with supporting packages. reflexio/server/README.md removes the Scripts section, updates LLM client module references to include embedding service components, and removes profile_updater from the Profile Generation pipeline. reflexio/server/services/README.md updates the extraction/ module list.

Changes

Documentation Sync

Layer / File(s)	Summary
Root README: lib section, server paths, storage, and supporting packages reflexio/README.md	Reworks the Code Map overview; adds a lib section for synchronous direct service calls; refreshes server entry-point paths (server/api.py, server/api_endpoints/, server/services/generation_service.py) and the component relationship diagram; updates storage/ to describe an abstract layer with split BaseStorage interfaces; replaces data/ documentation with a supporting packages section covering defaults, test support, and benchmarks.
Server README: LLM client modules, Scripts removal, and Profile Generation pipeline reflexio/server/README.md	Removes the Scripts TOC entry and section body; replaces legacy OpenAI/Claude client references with local embedding service, provider, and CLI daemon entries; clarifies embedding routing; removes profile_updater from the documented Profile Generation pipeline, shifting finalization responsibility to ProfileGenerationService.
Services README: extraction module list reflexio/server/services/README.md	Replaces tools.py, plan.py, and invariants.py with agent_run_records.py and outcome.py in the extraction/ directory listing.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~5 minutes

Possibly related PRs

• ReflexioAI/reflexio#135: Modifies the same reflexio/server/README.md and reflexio/server/services/README.md files, updating services directory index and entry listings.
• ReflexioAI/reflexio#110: Updates the same reflexio/README.md and reflexio/server/README.md to resync documented component paths and "Key Components" descriptions.

Poem

🐇 Hop hop, the docs now gleam,
Old scripts and data/ swept downstream.
lib leaps past FastAPI's gate,
Embeddings route — no clients to hate!
The map is true, the paths align —
This rabbit thinks the README's fine! ✨

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'docs: sync README files with latest repo state' accurately and concisely describes the main change: updating documentation files to reflect the current repository structure.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch docs/sync-readmes-20260615

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[coderabbitai]

Caution

Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (1)

reflexio/server/README.md (1)

225-288: ⚠️ Potential issue | 🟠 Major

Update the Mermaid diagram at line 519 to remove the ProfileUpdater node, aligning it with the documented flow.

The documented flow at line 235 explicitly states: Interactions → ProfileExtractor → ProfileDeduplicator → ProfileGenerationService finalization → Storage with no mention of ProfileUpdater. However, the Mermaid diagram at line 519 includes PD --> PU[ProfileUpdater]. Additionally, a codebase search found no references to profile_updater.py in Python files, confirming the diagram is outdated. Update the diagram to flow directly from ProfileDeduplicator to the finalization step or storage, matching the documented architecture.

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@reflexio/server/README.md` around lines 225 - 288, The Mermaid diagram
includes a ProfileUpdater node in the flow that contradicts the documented
architecture which flows directly from ProfileDeduplicator to
ProfileGenerationService finalization to Storage. Remove the ProfileUpdater node
(the line containing PD --> PU[ProfileUpdater]) from the Mermaid diagram and
update the flow to connect ProfileDeduplicator directly to the finalization step
or storage, ensuring the diagram aligns with the documented flow described in
the Profile Generation section.

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Outside diff comments:
In `@reflexio/server/README.md`:
- Around line 225-288: The Mermaid diagram includes a ProfileUpdater node in the
flow that contradicts the documented architecture which flows directly from
ProfileDeduplicator to ProfileGenerationService finalization to Storage. Remove
the ProfileUpdater node (the line containing PD --> PU[ProfileUpdater]) from the
Mermaid diagram and update the flow to connect ProfileDeduplicator directly to
the finalization step or storage, ensuring the diagram aligns with the
documented flow described in the Profile Generation section.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Path: .coderabbit.yaml

Review profile: CHILL

Plan: Pro Plus

Run ID: 15e7d424-66dd-43fd-994f-383a2c5ea583

📥 Commits

Reviewing files that changed from the base of the PR and between e5ef12c and 1b35c2b.

📒 Files selected for processing (3)

• reflexio/README.md
• reflexio/server/README.md
• reflexio/server/services/README.md