Remove workspace aliases in favor of namespaces

Author: tae2089

AGENTS.md

@@ -4,7 +4,7 @@ A local code analysis tool that parses codebases with Tree-sitter and builds a k
 
 ## MCP Server
 
-The ccg MCP server registered in `.mcp.json` provides 35 tools:
+The ccg MCP server registered in `.mcp.json` provides 33 tools:
 
 - `parse_project`, `build_or_update_graph`, `run_postprocess`
 - `get_postprocess_policy`, `reset_postprocess_policy`
@@ -16,7 +16,6 @@ The ccg MCP server registered in `.mcp.json` provides 35 tools:
 - `get_annotation`
 - `build_rag_index`, `get_rag_tree`, `get_doc_content`, `search_docs`, `retrieve_docs`
 - `upload_file`, `upload_files`, `list_namespaces`, `list_files`, `delete_file`, `delete_namespace`
-- `list_workspaces`, `delete_workspace` (deprecated aliases)
 
 `ccg serve` is the local stdio MCP entry point. Self-hosted HTTP mode is provided by
 the separate `ccg-server` binary, which serves `/mcp`, `/health`, `/ready`, `/status`,
@@ -35,7 +34,7 @@ Graceful shutdown: SIGINT/SIGTERM propagates context cancellation to in-progress
 | `/ccg-analyze`   | Code analysis: impact radius, flow tracing, dead code, architecture                          |
 | `/ccg-annotate`  | Annotation system: AI annotation workflow and tag reference                                  |
 | `/ccg-docs`      | Documentation: doc generation, RAG indexing, lint                                            |
-| `/ccg-workspace` | Namespace file management: upload, list, delete (`workspace` is a deprecated alias)          |
+| `/ccg-namespace` | Namespace file management: upload, list, delete                                              |
 
 Skill files are located under `skills/` and are written so coding agents such as Codex and Claude Code
 can use them as slash-command style workflows.
@@ -70,7 +69,7 @@ use ccg MCP tools and Agent Skills first.
 See the `guide/` directory for detailed documentation:
 
 - [CLI Reference](guide/cli-reference.md) - all commands, flags, and config files
-- [MCP Tools](guide/mcp-tools.md) - 35 MCP tools, Agent Skills, AI-Driven Annotation
+- [MCP Tools](guide/mcp-tools.md) - 33 MCP tools, Agent Skills, AI-Driven Annotation
 - [Annotations](guide/annotations.md) - annotation tags, examples, and search
 - [Webhook](guide/webhook.md) - webhook sync, branch filtering, HMAC, graceful shutdown
 - [Docker](guide/docker.md) - Docker builds, MCP server, PostgreSQL deployment

Dockerfile

@@ -26,14 +26,14 @@ FROM alpine:3.21
 RUN apk add --no-cache ca-certificates git \
     && addgroup -S ccg \
     && adduser -S -G ccg -h /home/ccg ccg \
-    && mkdir -p /workspace /repos /home/ccg/.cache /home/ccg/.config/ccg \
-    && chown -R ccg:ccg /workspace /repos /home/ccg
+    && mkdir -p /repo /repos /home/ccg/.cache /home/ccg/.config/ccg \
+    && chown -R ccg:ccg /repo /repos /home/ccg
 
 COPY --from=builder /usr/local/bin/ccg /usr/local/bin/ccg
 COPY --from=builder /usr/local/bin/ccg-server /usr/local/bin/ccg-server
 COPY --from=wiki-builder /src/web/wiki/dist /usr/share/ccg/wiki
 
-WORKDIR /workspace
+WORKDIR /repo
 USER ccg
 ENV HOME=/home/ccg \
     XDG_CACHE_HOME=/home/ccg/.cache \

README.md

@@ -1,6 +1,6 @@
 # code-context-graph
 
-Local code analysis tool that parses codebases via Tree-sitter into a knowledge graph. Supports 12 languages, 35 MCP tools, and custom annotation search.
+Local code analysis tool that parses codebases via Tree-sitter into a knowledge graph. Supports 12 languages, 33 MCP tools, and custom annotation search.
 
 CCG is built primarily for GPT, Claude, Codex, and other LLM-based coding agents. It acts as local or self-hosted context infrastructure: agents can search code by intent, inspect call graphs, trace impact, retrieve docs, and keep responses bounded instead of reading entire repositories into context.
 
@@ -11,7 +11,7 @@ Inspired by [code-review-graph](https://github.com/tirth8205/code-review-graph)
 ## Features
 
 - **12 languages**: Go, Python, TypeScript, Java, Ruby, JavaScript, C, C++, Rust, Kotlin, PHP, Lua/Luau
-- **35 MCP tools**: parse, search, impact analysis, flow tracing, dead code detection, postprocess operations, namespace file management, and more
+- **33 MCP tools**: parse, search, impact analysis, flow tracing, dead code detection, postprocess operations, namespace file management, and more
 - **RAG-first code exploration**: generated docs + community structure let LLM agents answer natural-language questions before drilling into exact graph nodes
 - **Browser Wiki UI**: `ccg-server` can serve generated docs, tree search, PageIndex-style retrieval, Context Tray copying, and an Obsidian-style graph viewer
 - **Custom annotations**: `@intent`, `@domainRule`, `@sideEffect`, `@mutates`, `@index` — search code by business context ([details](guide/annotations.md))
@@ -253,7 +253,7 @@ server can also expose `/wiki` when `--wiki-dir` is configured:
 ```
 
 MCP-capable clients such as Codex or Claude Code can connect and get access to
-35 MCP tools. See [MCP Tools Reference](guide/mcp-tools.md) for the full list.
+33 MCP tools. See [MCP Tools Reference](guide/mcp-tools.md) for the full list.
 
 ## Architecture
 
@@ -281,7 +281,7 @@ See [Architecture Details](guide/architecture.md) for component breakdown and DB
 | [CLI Reference](guide/cli-reference.md) | All commands, flags, and config file (`.ccg.yaml`) |
 | [Eval](guide/eval.md) | Parser/search quality evaluation, golden corpus, and metrics |
 | [Lint](guide/lint.md) | Detailed `ccg lint` category reference, interpretation guide, and CI usage |
-| [MCP Tools](guide/mcp-tools.md) | 35 MCP tools, agent skills, AI-Driven Annotation |
+| [MCP Tools](guide/mcp-tools.md) | 33 MCP tools, agent skills, AI-Driven Annotation |
 | [Annotations](guide/annotations.md) | Annotation system — tags, examples, search |
 | [Webhook](guide/webhook.md) | Webhook sync, branch filtering, HMAC, graceful shutdown |
 | [Docker](guide/docker.md) | Docker build, MCP server, Wiki UI, PostgreSQL deployment |

cmd/ccg-server/main.go

@@ -86,10 +86,6 @@ func newRootCmd(rt *core.Runtime, serviceVersion string) *cobra.Command {
 			dbDriver = viper.GetString("db.driver")
 			dbDSN = viper.GetString("db.dsn")
 
-			if cfg.WorkspaceRoot != "" && !cmd.Flags().Changed("namespace-root") {
-				cfg.NamespaceRoot = cfg.WorkspaceRoot
-			}
-			cfg.WorkspaceRoot = cfg.NamespaceRoot
 			if cfg.MaxFileBytes == 0 {
 				cfg.MaxFileBytes = viper.GetInt64("parse.max_file_bytes")
 			}
@@ -135,7 +131,6 @@ func newRootCmd(rt *core.Runtime, serviceVersion string) *cobra.Command {
 	cmd.Flags().BoolVar(&cfg.Stateless, "stateless", false, "Stateless session management (for multi-instance deployments)")
 	cmd.Flags().StringVar(&cfg.WikiDir, "wiki-dir", cfg.WikiDir, "Directory containing built Wiki UI assets; enables /wiki when set")
 	cmd.Flags().StringVar(&cfg.NamespaceRoot, "namespace-root", cfg.NamespaceRoot, "Root directory for file namespaces")
-	cmd.Flags().StringVar(&cfg.WorkspaceRoot, "workspace-root", "", "Deprecated alias for --namespace-root")
 
 	cmd.Flags().IntVar(&cfg.WebhookWorkers, "webhook-workers", cfg.WebhookWorkers, "Number of webhook sync workers")
 	cmd.Flags().IntVar(&cfg.WebhookMaxTrackedRepos, "webhook-max-tracked-repos", cfg.WebhookMaxTrackedRepos, "Maximum repositories tracked by the webhook sync queue")

cmd/ccg/main.go

@@ -66,7 +66,6 @@ func main() {
 			NoCache:             cfg.NoCache,
 			OTELEndpoint:        cfg.OTELEndpoint,
 			NamespaceRoot:       cfg.NamespaceRoot,
-			WorkspaceRoot:       cfg.WorkspaceRoot,
 			MaxFileBytes:        cfg.MaxFileBytes,
 			MaxTotalParsedBytes: cfg.MaxTotalParsedBytes,
 			ServiceVersion:      version,

guide/README.md

@@ -17,7 +17,7 @@ Context Tray Markdown, or visually explore graph edges.
 | [CLI Reference](cli-reference.md) | Full CLI commands, options, and configuration file (`.ccg.yaml`) |
 | [Eval](eval.md) | Parser/search quality evaluation, golden corpus, and metrics |
 | [Lint](lint.md) | Detailed `ccg lint` category reference, interpretation guide, and CI usage |
-| [MCP Tools](mcp-tools.md) | 35 MCP tools, agent skills, RAG-first routing, AI-driven annotation |
+| [MCP Tools](mcp-tools.md) | 33 MCP tools, agent skills, RAG-first routing, AI-driven annotation |
 | [Annotations](annotations.md) | Custom annotation system — tags, examples, search/RAG quality |
 | [Webhook](webhook.md) | GitHub / Gitea webhook sync, branch filtering, graceful shutdown |
 | [Docker](docker.md) | Docker image build, MCP server setup, Wiki UI deployment, PostgreSQL integration |

guide/architecture.md

@@ -74,7 +74,7 @@ Golden corpus-based parser accuracy and search quality evaluation framework.
 
 ### MCP Server (`internal/mcp/`)
 
-Exposes 35 tools via MCP protocol. The local `ccg serve` command exposes these
+Exposes 33 tools via MCP protocol. The local `ccg serve` command exposes these
 tools over stdio. The self-hosted `ccg-server` binary exposes the same tool
 surface over Streamable HTTP and adds health/status/webhook endpoints.
 

guide/claude-md-guide.md

@@ -35,7 +35,7 @@ get_minimal_context          ← always start here (graph state + recommended to
 
 - `search` covers annotations (`@intent`, `@domainRule`, etc.) as well as code
 - Narrow the scope with a path: `search(path: "internal/auth")`
-- In MSA environments, use the `namespace` parameter on all tools to isolate services (`workspace` remains a deprecated alias)
+- In MSA environments, use the `namespace` parameter on all tools to isolate services.
 ````
 
 ---

guide/cli-reference.md

@@ -141,8 +141,7 @@ recovery.
 | `ccg serve --cache-ttl <dur>` | TTL for MCP serve session cache (default `5m`; use `0` or `--no-cache` to disable) |
 | `ccg serve --no-cache` | Disable the in-memory MCP serve session cache |
 | `ccg serve --otel-endpoint <url>` | Enable OTLP HTTP trace export to the given full endpoint URL (for example `http://collector:4318/v1/traces`); when unset, CCG still creates SDK spans locally but does not export them |
-| `ccg serve --namespace-root <dir>` | Root directory for file namespaces (default `workspaces`) |
-| `ccg serve --workspace-root <dir>` | Deprecated alias for `--namespace-root` |
+| `ccg serve --namespace-root <dir>` | Root directory for file namespaces (default `namespaces`) |
 | `ccg serve --max-file-bytes <bytes>` | Maximum bytes allowed per parsed source file (`0` disables the limit) |
 | `ccg serve --max-total-parsed-bytes <bytes>` | Maximum total bytes parsed across source files (`0` disables the limit) |
 
@@ -156,8 +155,7 @@ HTTP MCP and webhook hosting now live in the dedicated `ccg-server` binary:
 | `ccg-server --insecure-http` | Allow non-loopback HTTP binding without a bearer token (testing only) |
 | `ccg-server --stateless` | Stateless session mode (multi-instance deployments) |
 | `ccg-server --wiki-dir <dir>` | Enable the browser Wiki UI at `/wiki` using a built React dist directory; `/wiki/api/*` uses the same bearer token as `/mcp` |
-| `ccg-server --namespace-root <dir>` | Root directory for file namespaces (default `workspaces`) |
-| `ccg-server --workspace-root <dir>` | Deprecated alias for `--namespace-root` |
+| `ccg-server --namespace-root <dir>` | Root directory for file namespaces (default `namespaces`) |
 | `ccg-server --allow-repo <pat>` | Allowed repo patterns for webhook sync (e.g. `org/*`, `org/api:main,develop`) |
 | `ccg-server --webhook-secret <s>` | HMAC secret for webhook signature verification |
 | `ccg-server --insecure-webhook` | Allow unsigned webhook requests for local testing only |

guide/development.md

@@ -117,7 +117,7 @@ internal/
   docs/               — Documentation generation
   eval/               — Parser/search quality evaluation (golden corpus, P/R/F1, P@K, MRR, nDCG)
   mcpruntime/         — Shared MCP runtime assembly, stdio runner, cache, telemetry
-  mcp/                — MCP server (35 tools)
+  mcp/                — MCP server (33 tools)
   wikiserver/         — ccg-server Wiki static serving and viewer API
   wikiindex/          — Wiki presentation index builder (`wiki-index.json`)
   model/              — DB models