docs: add thesis outline, chapter diagrams, and D2 skill

[singyichen]

Summary

• Add thesis outline (docs/thesis/outline.md) covering all 7 chapters of the Demo Paper
• Add 7 per-chapter D2 diagrams under docs/diagrams/thesis/ with PNG renders
• Add shared D2 base classes (docs/diagrams/shared/_base.d2) for consistent styling
• Install and enhance d2-diagram skill with project-specific guidelines

Changes

docs/thesis/

• outline.md — full 7-chapter thesis structure (Introduction → Ethics Statement)

docs/diagrams/

• shared/_base.d2 — shared style classes (base, tool, module, highlight, warning, step, store)
• thesis/thesis-ch1-introduction.d2/.png
• thesis/thesis-ch2-related-work.d2/.png
• thesis/thesis-ch3-system-design.d2/.png
• thesis/thesis-ch4-implementation.d2/.png
• thesis/thesis-ch5-experiments.d2/.png
• thesis/thesis-ch6-conclusion.d2/.png
• thesis/thesis-ch7-ethics.d2/.png

.claude/skills/

• d2-diagram/SKILL.md — updated with:
  • Standard classes block embedded (single source of truth)
  • Reserved keyword table (e.g. steps, scenarios cause compile errors)
  • Icon namespace restrictions (dev/* only; essentials/* returns 403)
  • Recommended render: --theme=300 --layout=elk --pad=50
  • Cross-file import pattern via ...@../shared/_base

Test Plan

• All 7 chapter diagrams render successfully with --theme=300 --layout=elk
• ...@../shared/_base import path resolves correctly after moving to thesis/ subfolder
• PNG outputs verified (2–5 MB each)
• No reserved keyword compile errors

🤖 Generated with Claude Code

[qodo-code-review]

Review Summary by Qodo

Add thesis outline, chapter diagrams, and D2 diagram skill documentation

📝 Documentation ✨ Enhancement

Walkthroughs

Description

• Add comprehensive D2 diagram skill guide with syntax, classes, and rendering options
• Create shared D2 base classes file for consistent styling across diagrams
• Add 7 thesis chapter diagrams covering introduction through ethics statement
• Add complete thesis outline documenting all chapters and research contributions

Diagram

flowchart LR
  A["D2 Skill Guide"] --> B["Shared Base Classes"]
  B --> C["7 Chapter Diagrams"]
  A --> D["Rendering Guidelines"]
  C --> E["Thesis Outline"]
  D --> F["Theme & Layout Options"]

Loading

File Changes

1. .claude/skills/adamelliotfields-skills-d2-diagram/SKILL.md 📝 Documentation +349/-0

Comprehensive D2 diagram skill guide with best practices

.claude/skills/adamelliotfields-skills-d2-diagram/SKILL.md

---

2. docs/diagrams/shared/_base.d2 ⚙️ Configuration changes +80/-0

Shared D2 style classes for consistent diagram styling

docs/diagrams/shared/_base.d2

---

3. docs/diagrams/thesis/thesis-ch1-introduction.d2 ✨ Enhancement +58/-0

Chapter 1 diagram showing research motivation and contributions

docs/diagrams/thesis/thesis-ch1-introduction.d2

---

View more (7)

4. docs/diagrams/thesis/thesis-ch2-related-work.d2 ✨ Enhancement +66/-0

Chapter 2 diagram covering platform survey and evaluation mechanisms

docs/diagrams/thesis/thesis-ch2-related-work.d2

---

5. docs/diagrams/thesis/thesis-ch3-system-design.d2 ✨ Enhancement +64/-0

Chapter 3 diagram illustrating system architecture and modules

docs/diagrams/thesis/thesis-ch3-system-design.d2

---

6. docs/diagrams/thesis/thesis-ch4-implementation.d2 ✨ Enhancement +78/-0

Chapter 4 diagram showing technology stack and implementation flow

docs/diagrams/thesis/thesis-ch4-implementation.d2

---

7. docs/diagrams/thesis/thesis-ch5-experiments.d2 ✨ Enhancement +69/-0

Chapter 5 diagram depicting experimental scenarios and evaluation methods

docs/diagrams/thesis/thesis-ch5-experiments.d2

---

8. docs/diagrams/thesis/thesis-ch6-conclusion.d2 ✨ Enhancement +44/-0

Chapter 6 diagram summarizing conclusions and future work directions

docs/diagrams/thesis/thesis-ch6-conclusion.d2

---

9. docs/diagrams/thesis/thesis-ch7-ethics.d2 ✨ Enhancement +67/-0

Chapter 7 diagram addressing privacy, consent, and data protection

docs/diagrams/thesis/thesis-ch7-ethics.d2

---

10. docs/thesis/outline.md 📝 Documentation +160/-0

Complete 7-chapter thesis outline with detailed section descriptions

docs/thesis/outline.md

---

[qodo-code-review]

Code Review by Qodo

🐞 Bugs (0) 📘 Rule violations (0) 📎 Requirement gaps (0) 📐 Spec deviations (0)

1. Skills index now stale ☑ 🐞 Bug ⚙ Maintainability

Description

A new skill is added (name: d2-diagram) but the repo’s skills catalog still claims 27 total skills
and its directory structure/quick reference omit this skill, making the documented skill inventory
incorrect.

Code

.claude/skills/adamelliotfields-skills-d2-diagram/SKILL.md[R1-4]

+---
+name: d2-diagram
+description: Generate diagrams using the D2 diagramming language. Use when the user requests diagrams.
+---

Evidence

The PR introduces a new skill via SKILL.md frontmatter, while the existing skills index explicitly
documents a fixed total (27) and a directory structure that does not include this new skill, so the
index is now inaccurate.

.claude/skills/adamelliotfields-skills-d2-diagram/SKILL.md[1-4]
.claude/SKILLS.md[19-53]
.claude/SKILLS.md[169-177]
.claude/SKILLS.md[223-224]

Agent prompt

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

## Issue description
A new skill (`d2-diagram`) was added, but `.claude/SKILLS.md` still documents **27** total skills and does not list the new skill in the directory structure and quick reference tables.
## Issue Context
`.claude/SKILLS.md` appears to be the project’s authoritative index of available skills and their organization. Adding a skill without updating this index creates confusion for developers and undermines the doc’s reliability.
## Fix Focus Areas
- .claude/SKILLS.md[19-56]
- .claude/SKILLS.md[167-177]
- .claude/SKILLS.md[223-224]
- .claude/skills/adamelliotfields-skills-d2-diagram/SKILL.md[1-4]
## Expected change
- Update the total skill count (27 → 28).
- Add the new skill to the appropriate section(s) of the directory structure and quick reference.
- Update the “Last Updated” metadata accordingly.

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

---

2. Skill folder/name mismatch ☑ 🐞 Bug ⚙ Maintainability

Description

The new skill’s folder name (adamelliotfields-skills-d2-diagram) does not match the declared skill
name (d2-diagram) and is not placed under the documented domain folders, making skill organization
inconsistent with the rest of the repo.

Code

.claude/skills/adamelliotfields-skills-d2-diagram/SKILL.md[R1-4]

+---
+name: d2-diagram
+description: Generate diagrams using the D2 diagramming language. Use when the user requests diagrams.
+---

Evidence

Existing skills follow a convention where the directory leaf matches the frontmatter name (e.g.,
api-spec), and .claude/SKILLS.md documents domain-grouped skill folders; the new skill deviates
from both conventions.

.claude/skills/adamelliotfields-skills-d2-diagram/SKILL.md[1-4]
.claude/skills/system-design/api-spec/SKILL.md[1-4]
.claude/SKILLS.md[19-53]

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 new skill declares `name: d2-diagram`, but its directory name and placement don’t follow the established `.claude/skills/<domain>/<skill-name>/SKILL.md` organization used across the repo. This makes the skills tree harder to navigate and may cause inconsistent discovery/invocation conventions.
## Issue Context
All existing skills appear domain-grouped and named consistently (directory leaf == frontmatter name). The new skill is introduced at a top-level folder with a prefixed name.
## Fix Focus Areas
- .claude/skills/adamelliotfields-skills-d2-diagram/SKILL.md[1-4]
- .claude/skills/system-design/api-spec/SKILL.md[1-4]
- .claude/SKILLS.md[19-53]
## Suggested change
- Move/rename the skill folder so the leaf directory matches `d2-diagram` (e.g., `.claude/skills/system-design/d2-diagram/SKILL.md` or a new domain folder if preferred).
- Update `.claude/SKILLS.md` to reflect the new location.

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

---

3. Duplicated D2 style source ☑ 🐞 Bug ⚙ Maintainability

Description

The standard D2 classes block is duplicated in the skill documentation and in
docs/diagrams/shared/_base.d2, creating multiple sources of truth that can drift and break styling
consistency over time.

Code

.claude/skills/adamelliotfields-skills-d2-diagram/SKILL.md[R112-195]

+Always include the following **standard class block** at the top of every `.d2` file. This is the project-wide base style:
+
+```d2
+classes: {
+  base: {
+    style: {
+      bold: true
+      font-size: 24
+    }
+  }
+
+  person: {
+    shape: person
+  }
+
+  animated: {
+    style: {
+      animated: true
+    }
+  }
+
+  multiple: {
+    style: {
+      multiple: true      # stacked visual — conveys "many instances"
+    }
+  }
+
+  tool: {
+    style: {
+      bold: true
+      font-size: 22
+      fill: PapayaWhip
+      fill-pattern: grain
+      border-radius: 8
+    }
+  }
+
+  module: {
+    style: {
+      bold: true
+      font-size: 22
+      fill: honeydew
+      fill-pattern: grain
+      border-radius: 8
+    }
+  }
+
+  highlight: {
+    style: {
+      bold: true
+      font-size: 22
+      fill: LightCyan
+      fill-pattern: grain
+      border-radius: 8
+    }
+  }
+
+  warning: {
+    shape: diamond
+    style: {
+      bold: true
+      font-size: 20
+      fill: MistyRose
+    }
+  }
+
+  step: {
+    shape: step
+    style: {
+      bold: true
+      font-size: 20
+    }
+  }
+
+  store: {
+    shape: cylinder
+    style: {
+      bold: true
+      font-size: 22
+      font: mono
+    }
+  }
+}
+```

Evidence

The exact same classes definitions exist in both the skill doc and the shared _base.d2. The
skill doc itself also instructs not to duplicate the classes block when _base.d2 exists, which
conflicts with keeping a full embedded copy.

.claude/skills/adamelliotfields-skills-d2-diagram/SKILL.md[114-195]
.claude/skills/adamelliotfields-skills-d2-diagram/SKILL.md[221-237]
docs/diagrams/shared/_base.d2[1-80]

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 project’s base D2 styles are duplicated in two places:
1) Embedded in the d2-diagram skill documentation
2) Stored in `docs/diagrams/shared/_base.d2`
This creates drift risk: future edits may update one but not the other.
## Issue Context
The skill doc already recommends importing `_base.d2` instead of repeating the classes block, yet it also contains the full block.
## Fix Focus Areas
- .claude/skills/adamelliotfields-skills-d2-diagram/SKILL.md[112-195]
- .claude/skills/adamelliotfields-skills-d2-diagram/SKILL.md[221-237]
- docs/diagrams/shared/_base.d2[1-80]
## Suggested change
Choose a single canonical source:
- Option A (recommended): Treat `docs/diagrams/shared/_base.d2` as canonical; in `SKILL.md`, replace the full block with a short snippet showing `...@../shared/_base` and a brief description of the available classes.
- Option B: Keep the block in `SKILL.md` as canonical and add a clear note that `_base.d2` must be kept in sync (or add a generator step/script if the repo supports it).

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

---

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