rollback: revert June 6th commits except cocoindex PATH fix, skill rework, and deps cleanup

Restores tree to 2a3e4be (last pre-June-6) plus:
- 4c7ae7b fix(pipeline): fall back to PATH lookup for cocoindex binary (#261)
- 584db63 rework skill and agent to combine RAG graph navigation with file-system search (#269)
- f512e87 remove requirements.txt, declare all deps in pyproject.toml (#271)

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Author: HumanBean17

AGENTS.md

@@ -154,15 +154,6 @@ The repo has a strong "propose then implement" culture (`propose/`,
 Skip this for clearly-bounded fixes (one-file bugs, doc edits, test
 loosening). Use judgement.
 
-When brainstorming produces a spec/design, write it as a proposal in
-`propose/active/<TOPIC>-PROPOSE.md` using the format established in
-`propose/completed/` (open a completed proposal there and match its
-section structure, headings, and level of detail — specific headings vary
-by proposal but always include: TL;DR, design principles, proposed
-surface/solution, risks and mitigations, decisions taken, tests, out of
-scope, migration plan). Do NOT use a brainstorming skill's default
-`docs/superpowers/specs/` location.
-
 ## Per-PR agent task contract
 
 When you're given a per-PR task prompt from `plans/AGENT-PROMPTS-*.md`

README.md

@@ -84,8 +84,6 @@ If vector hits come back and graph expansion adds neighbor symbols, the install
 
 ## Wire into an MCP host
 
-The server discovers your project automatically: it walks up from cwd looking for `.java-codebase-rag.yml` (or `.yaml`), like git finds `.git`. No env vars required if you have a YAML config in your project tree. For full precedence details, see [`docs/CONFIGURATION.md`](./docs/CONFIGURATION.md).
-
 ### Claude Code
 
 With the package installed, the console script `java-codebase-rag-mcp` is on your `PATH`. Register it project-scoped:
@@ -94,7 +92,7 @@ With the package installed, the console script `java-codebase-rag-mcp` is on you
 claude mcp add --transport stdio java-codebase-rag -- java-codebase-rag-mcp
 ```
 
-No env vars needed — the server walks up from cwd to find `.java-codebase-rag.yml`. For a minimal `.mcp.json` template, see [`mcp.json.example`](./mcp.json.example). Official docs: [Claude Code settings](https://docs.anthropic.com/en/docs/claude-code/settings).
+Then set env vars (`JAVA_CODEBASE_RAG_INDEX_DIR`, `JAVA_CODEBASE_RAG_SOURCE_ROOT`, `SBERT_MODEL`, …) in `.mcp.json` or your shell profile. For a project-scoped `.mcp.json` template, see [`mcp.json.example`](./mcp.json.example). Official docs: [Claude Code settings](https://docs.anthropic.com/en/docs/claude-code/settings).
 
 ### Claude Desktop
 
@@ -104,14 +102,16 @@ Edit `claude_desktop_config.json` (macOS: `~/Library/Application Support/Claude/
 {
   "mcpServers": {
     "java-codebase-rag": {
-      "command": "java-codebase-rag-mcp"
+      "command": "java-codebase-rag-mcp",
+      "env": {
+        "JAVA_CODEBASE_RAG_INDEX_DIR": "/ABSOLUTE/PATH/TO/.java-codebase-rag",
+        "JAVA_CODEBASE_RAG_SOURCE_ROOT": "/ABSOLUTE/PATH/TO/your-java-project"
+      }
     }
   }
 }
 ```
 
-The server discovers the project via walk-up from the cwd of the MCP host process. If your Java project is not the cwd, either set `JAVA_CODEBASE_RAG_SOURCE_ROOT` in the `env` block or add a `source_root` field to `.java-codebase-rag.yml` (see [`docs/CONFIGURATION.md`](./docs/CONFIGURATION.md)).
-
 See [`mcp.json.example`](./mcp.json.example) for the same shape in `.mcp.json` (Claude Code project-scoped) form.
 
 ### Driving the MCP from an agent