docs: add comprehensive 8-chapter technical documentation and glossary

[Kuldeep2822k]

Description

Adds complete, production-grade technical documentation covering the entire PALEE architecture, engine algorithms, storage layer, CLI commands, testing strategy, CI/CD pipeline, and planning specifications.

Key Highlights:

• 8 Core Chapters & Sub-pages (29 Markdown files) structured with hierarchical numeric ordering (01-0- through 08-2-, plus 09-glossary.md).
• Pure Solid-Black (#000000) Mermaid Diagrams: High-fidelity flowcharts, sequence diagrams, ER mappings, state machines, and DAG models.
• 100% Valid Relative Links: Clean intra-doc cross-references designed for Markdown viewers and static site deployment.
• .npmignore Protection: Ensured docs/ is excluded from published npm tarballs to keep production distribution minimal.

Type of Change

• docs: Documentation updates

Checklist

• Code compiles cleanly via npx tsc --noEmit
• All unit and invariant tests pass via npm test (135 tests passing across 18 suites)
• Production build succeeds via npm run build
• npm pack --dry-run produces clean package output
• Zero any casts in src/

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Review details

⚙️ Run configuration

Configuration used: Organization UI

Review profile: ASSERTIVE

Plan: Free

Run ID: 2c38fd8a-a229-4ff2-9051-5ef43d4c4388

📥 Commits

Reviewing files that changed from the base of the PR and between c773078 and 2b53abc.

📒 Files selected for processing (29)

• docs/01-0-overview.md
• docs/01-1-getting-started.md
• docs/01-2-architecture-overview.md
• docs/02-0-cli-commands.md
• docs/02-1-topic-management-commands.md
• docs/02-2-review-and-scheduling-commands.md
• docs/02-3-reporting-commands.md
• docs/02-4-session-management-command.md
• docs/03-0-engine-core.md
• docs/03-1-sm2-spaced-repetition-algorithm.md
• docs/03-2-dependency-graph-engine.md
• docs/04-0-storage-layer.md
• docs/04-1-frontmatter-parser-and-atomic-writes.md
• docs/04-2-file-locking.md
• docs/04-3-vault-walker-and-file-cache.md
• docs/04-4-session-memory-storage.md
• docs/05-0-data-model-and-types.md
• docs/05-1-topic-and-assessment-schema.md
• docs/05-2-configuration-and-cli-option-types.md
• docs/06-0-testing.md
• docs/06-1-unit-tests.md
• docs/06-2-integration-and-smoke-tests.md
• docs/07-0-cicd-and-release-pipeline.md
• docs/07-1-continuous-integration.md
• docs/07-2-release-workflow-and-npm-publishing.md
• docs/08-0-planning-and-design-documents.md
• docs/08-1-phase-1-specification-and-invariants.md
• docs/08-2-future-ai-module-and-phase-2-design.md
• docs/09-glossary.md

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: ASSERTIVE

Plan: Free

Run ID: 9aad85ac-7f08-4d2f-957f-ceeccdd6ce89

📥 Commits

Reviewing files that changed from the base of the PR and between e8b70e0 and c773078.

📒 Files selected for processing (30)

• .npmignore
• docs/01-0-overview.md
• docs/01-1-getting-started.md
• docs/01-2-architecture-overview.md
• docs/02-0-cli-commands.md
• docs/02-1-topic-management-commands.md
• docs/02-2-review-and-scheduling-commands.md
• docs/02-3-reporting-commands.md
• docs/02-4-session-management-command.md
• docs/03-0-engine-core.md
• docs/03-1-sm2-spaced-repetition-algorithm.md
• docs/03-2-dependency-graph-engine.md
• docs/04-0-storage-layer.md
• docs/04-1-frontmatter-parser-and-atomic-writes.md
• docs/04-2-file-locking.md
• docs/04-3-vault-walker-and-file-cache.md
• docs/04-4-session-memory-storage.md
• docs/05-0-data-model-and-types.md
• docs/05-1-topic-and-assessment-schema.md
• docs/05-2-configuration-and-cli-option-types.md
• docs/06-0-testing.md
• docs/06-1-unit-tests.md
• docs/06-2-integration-and-smoke-tests.md
• docs/07-0-cicd-and-release-pipeline.md
• docs/07-1-continuous-integration.md
• docs/07-2-release-workflow-and-npm-publishing.md
• docs/08-0-planning-and-design-documents.md
• docs/08-1-phase-1-specification-and-invariants.md
• docs/08-2-future-ai-module-and-phase-2-design.md
• docs/09-glossary.md

---

📝 Walkthrough

Summary by CodeRabbit

• Documentation
  • Added comprehensive documentation covering PALEE’s overview, setup, architecture, CLI commands, topic management, reviews, scheduling, reporting, sessions, storage, data models, testing, CI/CD, releases, planning, and glossary.
  • Added diagrams, command examples, workflows, configuration guidance, troubleshooting information, and references to help users understand and operate PALEE.
• Chores
  • Documentation files are now excluded from the published npm package, keeping the package distribution focused on runtime contents.

Walkthrough

Added a comprehensive PALEE documentation set covering architecture, commands, engine behavior, storage, data models, testing, CI/CD, planning, and terminology. Added docs/ to .npmignore.

Changes

PALEE documentation

Layer / File(s)	Summary
Project orientation and setup .npmignore, docs/01-*.md	Added project overview, installation, configuration, architecture, navigation, and package-content documentation.
CLI commands and workflows docs/02-*.md	Documented topic management, review, scheduling, reporting, validation, JSON output, and session commands.
Engine, schemas, and configuration docs/03-*.md, docs/05-*.md	Documented SM-2 scheduling, dependency graphs, data models, topic schemas, difficulty normalization, configuration, and CLI option types.
Storage safety and session persistence docs/04-*.md	Documented frontmatter handling, atomic writes, locking, vault traversal, caching, and session memory.
Testing, CI, and release documentation docs/06-*.md, docs/07-*.md	Documented test architecture, integration and smoke tests, CI workflows, security checks, packaging, and publishing.
Planning, future design, and glossary docs/08-*.md, docs/09-glossary.md	Added planning references, Phase 1 invariants, Phase 2 designs, and terminology definitions.

Estimated code review effort: 3 (Moderate) | ~25 minutes

Merge Risk: ⚪ Minimal · up to c7730

This change adds documentation and package-publishing metadata without any identified current-head correctness, security, availability, or deployment risk; no actionable merge-blocking risk remains after normal checks and review.

Poem

A rabbit reads the docs with care,
Through vaults and engines everywhere.
The package leaves the pages out,
While diagrams hop about.
“Clear paths ahead!” the rabbit sings.

---

Note

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[qodo-code-review]

PR Summary by Qodo

docs: add comprehensive technical docs (8 chapters) and glossary

📝 Documentation ⚙️ Configuration changes 🕐 40+ Minutes

AI Description

• Add 8-chapter technical documentation set spanning architecture, CLI, engine, storage, testing,
 and CI/CD.
• Provide a glossary plus cross-linked Mermaid diagrams mapping concepts to code entities.
• Exclude docs/ from npm tarballs via .npmignore to keep published artifacts minimal.

Diagram

graph TD
A["Engineers"] --> B["docs/"] --> C["Chapters 01-08"] --> D["09-glossary.md"]
B --> E["Mermaid diagrams"]
F[".npmignore"] --> G["npm pack"] --> H["Published tarball"]
B -.-> H

Loading

High-Level Assessment

The following are alternative approaches to this PR:

1. Publish docs as a separate static site (e.g., Docusaurus/MkDocs)

• ➕ Better navigation/search/versioning UX
• ➕ Easier to validate links/diagrams in CI
• ➕ Can publish without bloating repo root docs view
• ➖ Adds build tooling and hosting overhead
• ➖ Requires keeping site config in sync with repo structure

2. Generate API/reference docs from code comments (TypeDoc) and keep narrative docs minimal

• ➕ Reduces manual drift for type/API details
• ➕ Single source of truth for interfaces
• ➖ Does not replace architecture/operational narrative chapters
• ➖ Requires doc-comment discipline and tooling setup

3. Ship docs inside the npm package (do not ignore docs/)

• ➕ Docs available offline to all npm consumers by default
• ➕ Version-aligned docs with the installed CLI
• ➖ Increases package size for production installs
• ➖ Docs may be redundant for users who only need the binary

Recommendation: Current approach is a good fit: keep docs in-repo for maintainers while excluding them from npm artifacts to preserve a lean distribution. Consider adding (in a follow-up) a single docs index entry point in README and optional CI link checking/mermaid linting if documentation becomes a frequent change surface.

Files changed (30) +4132 / -0

Documentation (29) +4131 / -0

01-0-overview.mdAdd system overview and philosophy chapter +183/-0

Add system overview and philosophy chapter

• Introduces PALEE’s core goals, three-layer architecture framing, and concept-to-code mappings. Includes Mermaid diagrams to visualize entity relationships and system boundaries.

docs/01-0-overview.md

01-1-getting-started.mdAdd installation and initial configuration guide +160/-0

Add installation and initial configuration guide

• Documents npm installation, vault setup, optional AI provider configuration, and basic verification workflows. Links to key source files and specs for traceability.

docs/01-1-getting-started.md

01-2-architecture-overview.mdAdd detailed architecture overview and safety contract +124/-0

Add detailed architecture overview and safety contract

• Describes Storage/Engine/CLI layering, primary data flows, and the file-safety contract (atomic writes + OCC + locking). Includes flow/sequence diagrams for entity mapping and write flows.

docs/01-2-architecture-overview.md

02-0-cli-commands.mdAdd CLI command architecture and grouping guide +133/-0

Add CLI command architecture and grouping guide

• Explains commander-based command wiring, common execution patterns, exit codes, and command group taxonomy. Adds diagrams for execution flow and output/validation mapping.

docs/02-0-cli-commands.md

02-1-topic-management-commands.mdDocument topic management commands (adopt/roadmap/migrate) +143/-0

Document topic management commands (adopt/roadmap/migrate)

• Covers topic ingestion lifecycle and the safety/normalization steps for adopting notes and bulk imports. Includes diagrams showing note adoption and metadata injection flows.

docs/02-1-topic-management-commands.md

02-2-review-and-scheduling-commands.mdDocument review, next, and plan scheduling flows +127/-0

Document review, next, and plan scheduling flows

• Details how manual review updates SM-2 state, how due/ready topics are determined, and how scheduling is dependency-aware. Includes diagrams mapping CLI flows to engine functions.

docs/02-2-review-and-scheduling-commands.md

02-3-reporting-commands.mdDocument reporting and validation commands +150/-0

Document reporting and validation commands

• Describes dashboard/progress aggregation, mastery breakdowns, and graph integrity validation. Includes diagrams for data transformation from vault files to reported metrics.

docs/02-3-reporting-commands.md

02-4-session-management-command.mdDocument session lifecycle and working-memory handling +138/-0

Document session lifecycle and working-memory handling

• Explains session start/end flows, active-topic resolution, hot.md working memory, and draft recovery behavior. Links to relevant CLI and storage implementations.

docs/02-4-session-management-command.md

03-0-engine-core.mdAdd engine core overview and subsystem maps +118/-0

Add engine core overview and subsystem maps

• Introduces deterministic engine responsibilities and splits between SM-2 scheduling and dependency graph logic. Adds diagrams mapping engine API to internal functions and input/output data flow.

docs/03-0-engine-core.md

03-1-sm2-spaced-repetition-algorithm.mdDeep-dive on SM-2 algorithm rules and formulas +145/-0

Deep-dive on SM-2 algorithm rules and formulas

• Provides the quality scale, ease factor delta formula, interval progression, lapse behavior, and constraints used by the implementation. Serves as a reference aligned to engine code and tests.

docs/03-1-sm2-spaced-repetition-algorithm.md

03-2-dependency-graph-engine.mdDeep-dive on dependency DAG model and validation +148/-0

Deep-dive on dependency DAG model and validation

• Documents TopicNode structure, mastery thresholds, readiness filtering, and cycle/dangling-dependency detection. Anchors explanations to engine code paths and tests.

docs/03-2-dependency-graph-engine.md

04-0-storage-layer.mdAdd storage layer overview and component index +115/-0

Add storage layer overview and component index

• Summarizes the file-safety contract and maps storage components (frontmatter, atomic writes, locks, cache, walker, memory). Includes diagrams for architecture and review command interaction with storage.

docs/04-0-storage-layer.md

04-1-frontmatter-parser-and-atomic-writes.mdDocument CST-preserving frontmatter updates and atomic write flow +134/-0

Document CST-preserving frontmatter updates and atomic write flow

• Explains YAML CST parsing, preservation-aware updates, fingerprinting/OCC, and atomic write semantics (including platform quirks). References tests validating body/key/comment preservation.

docs/04-1-frontmatter-parser-and-atomic-writes.md

04-2-file-locking.mdDocument lock identity, heartbeat, and stale lock recovery +165/-0

Document lock identity, heartbeat, and stale lock recovery

• Details directory-based locking, path hashing, heartbeats, and platform-aware stale-lock handling. Includes diagrams mapping locking concepts to code entities.

docs/04-2-file-locking.md

04-3-vault-walker-and-file-cache.mdDocument vault traversal rules and cache validation logic +113/-0

Document vault traversal rules and cache validation logic

• Describes markdown discovery, exclusion rules, symlink/permission handling, and cache behavior for rapid edit cycles. Includes a discovery logic flow diagram.

docs/04-3-vault-walker-and-file-cache.md

04-4-session-memory-storage.mdDocument .palee session storage layout and IDs +129/-0

Document .palee session storage layout and IDs

• Explains the .palee directory schema, hot.md contract, session/draft ID generation, and durability/derived views. Links behaviors back to storage and CLI implementations.

docs/04-4-session-memory-storage.md

05-0-data-model-and-types.mdAdd data model/type-system reference chapter +135/-0

Add data model/type-system reference chapter

• Introduces core TypeScript interfaces and how they serialize to frontmatter/JSON. Includes diagrams mapping conceptual domain objects to src/types.ts entities.

docs/05-0-data-model-and-types.md

05-1-topic-and-assessment-schema.mdDocument Topic schema, assessments, and frontmatter fields +152/-0

Document Topic schema, assessments, and frontmatter fields

• Describes Topic attributes, schema versioning, IDs, lifecycle status, dependencies, and assessment structure. Provides adoption data-flow mapping to connect domain concepts to code.

docs/05-1-topic-and-assessment-schema.md

05-2-configuration-and-cli-option-types.mdDocument config storage and CLI option typing +144/-0

Document config storage and CLI option typing

• Explains PaleeConfig, config path resolution across platforms, environment overrides for tests, and type-safe CLI option structures. Anchors to relevant CLI and type definitions.

docs/05-2-configuration-and-cli-option-types.md

06-0-testing.mdAdd testing strategy overview +105/-0

Add testing strategy overview

• Summarizes the test stack (node:test, tsx, c8), isolation strategy via PALEE_CONFIG_DIR, and suite organization. Links to unit and integration test chapters.

docs/06-0-testing.md

06-1-unit-tests.mdDocument unit test coverage by subsystem +118/-0

Document unit test coverage by subsystem

• Details unit test intent across engine, storage, CLI utilities, and types, emphasizing determinism and defensive I/O invariants. References specific assertions tied to implementation behavior.

docs/06-1-unit-tests.md

06-2-integration-and-smoke-tests.mdDocument end-to-end CLI integration and smoke testing +129/-0

Document end-to-end CLI integration and smoke testing

• Explains fixture lifecycle, CLI execution harness, and validation of persistence/output contracts. Includes diagrams showing integration flow across temp vault storage and command pipelines.

docs/06-2-integration-and-smoke-tests.md

07-0-cicd-and-release-pipeline.mdAdd CI/CD and workflow orchestration overview +152/-0

Add CI/CD and workflow orchestration overview

• Provides a top-level map of GitHub Actions workflows, triggers, and responsibilities across CI, security, labeling, and releases. Includes workflow event mapping diagram.

docs/07-0-cicd-and-release-pipeline.md

07-1-continuous-integration.mdDocument CI jobs, matrices, and quality gates +165/-0

Document CI jobs, matrices, and quality gates

• Details CI workflow structure, concurrency, lint/typecheck/build checks, test matrices, and guardrails. Links to workflow files and supporting configuration.

docs/07-1-continuous-integration.md

07-2-release-workflow-and-npm-publishing.mdDocument release workflow, verification, and publish flow +128/-0

Document release workflow, verification, and publish flow

• Describes tag-triggered releases, version consistency checks, artifact verification, idempotent publish steps, and post-publish smoke testing. Includes diagrams of interactions with npm/GitHub releases.

docs/07-2-release-workflow-and-npm-publishing.md

08-0-planning-and-design-documents.mdAdd planning/design document index chapter +176/-0

Add planning/design document index chapter

• Creates an index into planning/ artifacts and summarizes how Phase 1/2 planning documents guide architecture and execution. Links to the Phase 1 and Phase 2 focused chapters.

docs/08-0-planning-and-design-documents.md

08-1-phase-1-specification-and-invariants.mdSummarize Phase 1 specs and safety invariants +137/-0

Summarize Phase 1 specs and safety invariants

• Documents the deterministic core requirements, layered architecture, and critical invariants (storage safety, SM-2 constraints, validation gates). Includes diagrams for command execution flow through layers.

docs/08-1-phase-1-specification-and-invariants.md

08-2-future-ai-module-and-phase-2-design.mdOutline future AI module architecture and Phase 2 direction +185/-0

Outline future AI module architecture and Phase 2 direction

• Describes planned AI tutoring/tooling architecture, human-confirmation gates, and known gaps driving Phase 2. Includes diagrams of the intended AI interaction loop and constraints.

docs/08-2-future-ai-module-and-phase-2-design.md

09-glossary.mdAdd glossary mapping domain terms to code and storage +180/-0

Add glossary mapping domain terms to code and storage

• Defines key PALEE concepts (SRS/SM-2, topics, DAG dependencies, atomic writes, locking, vault walking, sessions) and links each to concrete code references. Includes diagrams mapping natural language terms to implementation modules.

docs/09-glossary.md

Other (1) +1 / -0

.npmignoreExclude docs/ from npm package output +1/-0

Exclude docs/ from npm package output

• Adds docs/ to .npmignore so documentation is not bundled into published npm tarballs.

.npmignore

[qodo-code-review]

Code Review by Qodo

🐞 Bugs (0) 📘 Rule violations (0) 📜 Skill insights (0)

1. Broken docs links ✓ Resolved 🐞 Bug ≡ Correctness

Description

docs/07-2-release-workflow-and-npm-publishing.md includes Markdown links whose URLs contain an
embedded space (e.g. .../blob/<sha>/ .github/...), which will render as broken/404 links. This
prevents readers from navigating to the referenced workflow/scripts from the documentation.

Code

docs/07-2-release-workflow-and-npm-publishing.md[17]

+The pipeline is triggered by the push of a tag matching the `v*.*.*` pattern or via manual `workflow_dispatch`[ .github/workflows/release.yml#3-7](https://github.com/Kuldeep2822k/cli/blob/e8b70e0d/ .github/workflows/release.yml#L3-L7) To prevent race conditions during publishing, it uses a concurrency group `release-production` with `cancel-in-progress: false`[ .github/workflows/release.yml#9-11](https://github.com/Kuldeep2822k/cli/blob/e8b70e0d/ .github/workflows/release.yml#L9-L11)

Relevance

●●● Strong

Links with embedded spaces are objectively broken; correctness fix aligns with docs quality claims.

PR-#58

ⓘ Recommendations generated based on similar findings in past PRs

Evidence

The affected links include a space after the commit SHA in the URL (.../blob/e8b70e0d/ .github/...
and .../blob/e8b70e0d/ scripts/...), which is not a valid GitHub file path and will not resolve as
intended.

docs/07-2-release-workflow-and-npm-publishing.md[17-17]
docs/07-2-release-workflow-and-npm-publishing.md[50-50]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

### Issue description
Several Markdown links in `docs/07-2-release-workflow-and-npm-publishing.md` contain a literal space inside the URL path (e.g. between `/blob/<sha>/` and `.github/...`). This produces invalid GitHub paths and results in broken links.

### Issue Context
This is a docs-only change, but the file currently contains multiple affected links (the initial paragraph and the various `Sources:` lines).

### Fix Focus Areas
- docs/07-2-release-workflow-and-npm-publishing.md[17-17]
- docs/07-2-release-workflow-and-npm-publishing.md[50-50]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

2. Commit-pinned source links ✓ Resolved 🐞 Bug ⚙ Maintainability

Description

Many docs pages link to source files using absolute GitHub URLs pinned to a specific repo + commit
SHA, which reduces portability (forks/offline/static-site) and will become stale as the code
changes. Readers will be taken to an old snapshot instead of the current implementation.

Code

docs/01-0-overview.md[R4-5]

+- [README.md](https://github.com/Kuldeep2822k/cli/blob/e8b70e0d/README.md?plain=1)
+- [bin/palee.ts](https://github.com/Kuldeep2822k/cli/blob/e8b70e0d/bin/palee.ts)

Relevance

●●● Strong

Repo-owner/commit-pinned URLs will stale and contradict stated “relative links” goal; likely to be
updated.

PR-#58

ⓘ Recommendations generated based on similar findings in past PRs

Evidence

The documentation links directly to https://github.com/Kuldeep2822k/cli/blob/e8b70e0d/... rather
than using repo-relative links or a moving branch/tag reference, making the docs snapshot-specific
and repo-owner-specific.

docs/01-0-overview.md[4-8]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

### Issue description
The docs’ “Relevant source files” sections frequently use absolute GitHub `blob/<sha>` links hardcoded to a single repository owner and commit. This limits usefulness outside GitHub (offline/static site), and for a living documentation set, it will point readers at outdated code.

### Issue Context
If the intent is versioned docs, consider moving these links to `blob/vX.Y.Z/...` (tag) during release. If the intent is always-current docs, prefer repo-relative links or `blob/main/...`.

### Fix Focus Areas
- docs/01-0-overview.md[4-8]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

3. BOM in markdown files ✓ Resolved 🐞 Bug ⚙ Maintainability

Description

Several new docs files start with a UTF-8 BOM character before the leading #, creating
inconsistent file bytes and risking subtle incompatibilities with simpler Markdown tooling/linters.
This also makes diffs and text-processing less predictable across platforms.

Code

docs/01-0-overview.md[1]

+# Overview

Relevance

●●● Strong

Removing UTF-8 BOM is a trivial, deterministic docs hygiene fix; team usually accepts such cleanups.

PR-#58

ⓘ Recommendations generated based on similar findings in past PRs

Evidence

Multiple docs files display as # ... at line 1 in the checked-out branch, which indicates an
extra BOM character preceding #.

docs/01-0-overview.md[1-1]
docs/03-0-engine-core.md[1-1]
docs/07-0-cicd-and-release-pipeline.md[1-1]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

### Issue description
Some documentation files begin with a UTF-8 BOM (U+FEFF) before the first `#` heading. While many renderers tolerate this, it introduces inconsistent encoding markers and can confuse less robust tooling.

### Issue Context
The BOM appears in multiple files but not all, indicating inconsistent generation/encoding.

### Fix Focus Areas
- docs/01-0-overview.md[1-1]
- docs/03-0-engine-core.md[1-1]
- docs/07-0-cicd-and-release-pipeline.md[1-1]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

Context

Review mode: ⚖️ Balanced: Although the PR spans many documentation files and links, it is primarily a large, shallow documentation addition with no production logic changes; a single careful review is sufficient.

Tip of the day

💡 Did you know, you can turn on the rule miner and Qodo learns your standards from review history

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