feat: move config.yaml and index.js into src/ — fixes #630

[avoidwork]

Description

Moved root-level files (config.yaml and index.js) into the src/ directory to eliminate structural inconsistency and align with the existing codebase organization.

Type of Change

• Bugfix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update
• Refactor (no functional changes)
• CI / build / tooling

Testing

• All 1043 tests pass
• Lint passes clean (oxlint + oxfmt)
• Application starts successfully: node src/index.js --mode chat "test"

Coverage

• Line coverage maintained

Checklist

• npm run lint passes
• Tests pass with maintained line coverage
• No forbidden patterns used
• Conventional Commit style applied

Changes

File	Change
config.yaml	Moved to src/config.yaml
index.js	Moved to src/index.js
Dockerfile	Removed root-level COPY lines, updated entrypoint to src/index.js
package.json	Removed from files, updated main, bin, start
src/config/loader.js	Simplified config path from ../../config.yaml to ../config.yaml
src/index.js	Updated all 20 import paths from ./src/ to ./, fixed package.json import to ../package.json
src/tui/contextTokens.js	Updated comment reference
src/session/checkpointer.js	Updated JSDoc reference

Audit Against Issue #630

Requirement	Status	Notes
Move config.yaml into src/	Done	Moved to src/config.yaml (src root, not nested in src/config/)
Move index.js into src/	Done	Moved to src/index.js
Update import paths	Done	All 20 imports in index.js, loader.js config path, package.json references
Update Dockerfile	Done	Removed root-level COPY lines, updated entrypoint
Update package.json	Done	files array, main, bin, start all updated
Cosmetic references	Done	contextTokens.js comment, checkpointer.js JSDoc
Test pass	Done	1043/1043 passing
Lint pass	Done	0 warnings, 0 errors

Related Issue

Fixes #630

[avoidwork]

Audit Against Issue #630

Issue: feat: restructure app with discrete backends and move root files to src
Status: All requirements implemented and verified.

Requirements Checklist

#	Requirement	Status	Notes
1	Move config.yaml from project root into src/	Done	Moved to src/config.yaml (src root, not nested in src/config/)
2	Move index.js from project root into src/	Done	Moved to src/index.js
3	Update all import paths and references	Done	20 imports in index.js, loader.js config path, package.json references
4	Update Dockerfile and build scripts	Done	Removed root-level COPY lines, updated entrypoint to src/index.js

Audit Findings from Issue #630

Finding	Status	Resolution
src/config/loader.js:12 — hardcoded path	Done	../../config.yaml → ../config.yaml
Dockerfile:13,41 — COPY config.yaml	Done	Removed both COPY lines (files now inside src/)
package.json:27,29 — files array	Done	Removed index.js and config.yaml from files
package.json:38,39,41 — main/bin/start	Done	All point to src/index.js
Dockerfile:26 — entrypoint	Done	Updated to src/index.js
src/tui/contextTokens.js:6 — comment	Done	Updated comment reference
src/session/checkpointer.js:5 — JSDoc	Done	Updated JSDoc reference
src/agent/backends/* — import chains	Done	No changes needed — imports are relative to src/
src/workspace/loadAgents.js — path traversal	Done	No changes needed — uses cwd-based resolution

Verification

• Tests: 1043/1043 passing
• Lint: 0 warnings, 0 errors (oxlint + oxfmt)
• Startup: node src/index.js --mode chat test runs successfully

Files Changed (11 files, 66 insertions, 57 deletions)

src/config.yaml (renamed from config.yaml)
src/index.js (renamed from index.js, 20 import paths updated)
src/config/loader.js (config path simplified)
Dockerfile (COPY lines removed, entrypoint updated)
package.json (files, main, bin, start updated)
src/tui/contextTokens.js (comment)
src/session/checkpointer.js (JSDoc)

No functional changes — purely structural reorganization.