Refactor application path handling and data storage architecture

Replace simple directory-based path system with git-aware data management that uses global data directories and proper workspace detection.

🤖 Generated with opencode
Co-Authored-By: opencode <noreply@opencode.ai>

packages/opencode/src/tool/glob.ts

@@ -51,7 +51,7 @@ export const GlobTool = Tool.define({
   }),
   async execute(params) {
     const app = await App.use()
-    const search = params.path || app.root
+    const search = params.path || app.path.cwd
     const limit = 100
     const glob = new Bun.Glob(params.pattern)
     const files = []

packages/opencode/src/tool/grep.ts

@@ -287,7 +287,7 @@ export const GrepTool = Tool.define({
     }
 
     const app = await App.use()
-    const searchPath = params.path || app.root
+    const searchPath = params.path || app.path.cwd
 
     // If literalText is true, escape the pattern
     const searchPattern = params.literalText

packages/opencode/src/tool/ls.ts

@@ -26,7 +26,7 @@ export const ListTool = Tool.define({
   }),
   async execute(params) {
     const app = await App.use()
-    const searchPath = path.resolve(app.root, params.path || ".")
+    const searchPath = path.resolve(app.path.cwd, params.path || ".")
 
     const glob = new Bun.Glob("**/*")
     const files = []

packages/opencode/src/tool/lsp-diagnostics.ts

@@ -37,7 +37,7 @@ TIPS:
     const app = await App.use()
     const normalized = path.isAbsolute(args.path)
       ? args.path
-      : path.join(app.root, args.path)
+      : path.join(app.path.cwd, args.path)
     await LSP.file(normalized)
     const diagnostics = await LSP.diagnostics()
     const file = diagnostics[normalized]

packages/opencode/src/tool/lsp-hover.ts

@@ -21,7 +21,7 @@ export const LspHoverTool = Tool.define({
     const app = await App.use()
     const file = path.isAbsolute(args.file)
       ? args.file
-      : path.join(app.root, args.file)
+      : path.join(app.path.cwd, args.file)
     await LSP.file(file)
     const result = await LSP.hover({
       ...args,