diff --git a/lua/vectorcode/integrations/codecompanion/files_ls_tool.lua b/lua/vectorcode/integrations/codecompanion/files_ls_tool.lua
index d5a3c064..e5a940ff 100644
--- a/lua/vectorcode/integrations/codecompanion/files_ls_tool.lua
+++ b/lua/vectorcode/integrations/codecompanion/files_ls_tool.lua
@@ -10,7 +10,7 @@ local default_opts = {
 }
 
 ---@param opts VectorCode.CodeCompanion.FilesLsToolOpts
----@return CodeCompanion.Agent.Tool
+---@return CodeCompanion.Tools.Tool
 return function(opts)
   opts = vim.tbl_deep_extend("force", default_opts, opts or {})
   local job_runner =
@@ -18,14 +18,14 @@ return function(opts)
       opts.use_lsp
     )
   local tool_name = "vectorcode_files_ls"
-  ---@type CodeCompanion.Agent.Tool|{}
+  ---@type CodeCompanion.Tools.Tool|{}
   return {
     name = tool_name,
     cmds = {
-      ---@param agent CodeCompanion.Agent
+      ---@param tools CodeCompanion.Tools
       ---@param action {project_root: string}
       ---@return nil|{ status: string, data: string }
-      function(agent, action, _, cb)
+      function(tools, action, _, cb)
         local args = { "files", "ls", "--pipe" }
         if action ~= nil then
           action.project_root = action.project_root
@@ -50,7 +50,7 @@ return function(opts)
               data = error,
             })
           end
-        end, agent.chat.bufnr)
+        end, tools.chat.bufnr)
       end,
     },
     schema = {
@@ -70,9 +70,9 @@ return function(opts)
       },
     },
     output = {
-      ---@param agent CodeCompanion.Agent
+      ---@param tools CodeCompanion.Tools
       ---@param stdout string[][]
-      success = function(_, agent, _, stdout)
+      success = function(_, tools, _, stdout)
         stdout = stdout[1]
         local user_message
         for i, col in ipairs(stdout) do
@@ -82,8 +82,8 @@ return function(opts)
           else
             user_message = ""
           end
-          agent.chat:add_tool_output(
-            agent.tool,
+          tools.chat:add_tool_output(
+            tools.tool,
             string.format("<path>%s</path>", col),
             user_message
           )
diff --git a/lua/vectorcode/integrations/codecompanion/files_rm_tool.lua b/lua/vectorcode/integrations/codecompanion/files_rm_tool.lua
index cf8d44de..b14aa175 100644
--- a/lua/vectorcode/integrations/codecompanion/files_rm_tool.lua
+++ b/lua/vectorcode/integrations/codecompanion/files_rm_tool.lua
@@ -12,14 +12,14 @@ local default_opts = {
 ---@alias FilesRmArgs { paths: string[], project_root: string }
 
 ---@param opts VectorCode.CodeCompanion.FilesRmToolOpts
----@return CodeCompanion.Agent.Tool
+---@return CodeCompanion.Tools
 return function(opts)
   opts = vim.tbl_deep_extend("force", default_opts, opts or {})
 
   local tool_name = "vectorcode_files_rm"
   local job_runner = cc_common.initialise_runner(opts.use_lsp)
 
-  ---@type CodeCompanion.Agent.Tool|{}
+  ---@type CodeCompanion.Tools|{}
   return {
     name = tool_name,
     schema = {
@@ -47,10 +47,10 @@ return function(opts)
       },
     },
     cmds = {
-      ---@param agent CodeCompanion.Agent
+      ---@param tools CodeCompanion.Tools
       ---@param action VectoriseToolArgs
       ---@return nil|{ status: string, data: string }
-      function(agent, action, _, cb)
+      function(tools, action, _, cb)
         local args = { "files", "rm", "--pipe" }
         local project_root = vim.fs.abspath(vim.fs.normalize(action.project_root or ""))
         if project_root ~= "" then
@@ -99,22 +99,22 @@ return function(opts)
               cb({ status = "error", data = { error = error, code = code } })
             end
           end,
-          agent.chat.bufnr
+          tools.chat.bufnr
         )
       end,
     },
     output = {
-      ---@param self CodeCompanion.Agent.Tool
+      ---@param self CodeCompanion.Tools.Tool
       prompt = function(self, _)
         return string.format(
           "Remove %d files from VectorCode database?",
           #self.args.paths
         )
       end,
-      ---@param self CodeCompanion.Agent.Tool
-      ---@param agent CodeCompanion.Agent
-      success = function(self, agent, _, _)
-        agent.chat:add_tool_output(self, "**VectorCode `files_rm` tool**: successful.")
+      ---@param self CodeCompanion.Tools.Tool
+      ---@param tools CodeCompanion.Tools
+      success = function(self, tools, _, _)
+        tools.chat:add_tool_output(self, "**VectorCode `files_rm` tool**: successful.")
       end,
     },
   }
diff --git a/lua/vectorcode/integrations/codecompanion/init.lua b/lua/vectorcode/integrations/codecompanion/init.lua
index 736d02ef..5358c18b 100644
--- a/lua/vectorcode/integrations/codecompanion/init.lua
+++ b/lua/vectorcode/integrations/codecompanion/init.lua
@@ -1,50 +1,10 @@
 ---@module "codecompanion"
 
-local vc_config = require("vectorcode.config")
-local check_cli_wrap = vc_config.check_cli_wrap
-
 return {
   chat = {
-    ---@param component_cb (fun(result:VectorCode.QueryResult):string)?
-    make_slash_command = check_cli_wrap(function(component_cb)
-      vim.deprecate(
-        "vectorcode slash command",
-        "vectorcode tool/extension",
-        "0.8.0",
-        "VectorCode",
-        true
-      )
-      return {
-        description = "Add relevant files from the codebase.",
-        ---@param chat CodeCompanion.Chat
-        callback = function(chat)
-          local codebase_prompt = ""
-          local vc_cache = vc_config.get_cacher_backend()
-          local bufnr = chat.context.bufnr
-          if not vc_cache.buf_is_registered(bufnr) then
-            return
-          end
-          codebase_prompt =
-            "The following are relevant files from the repository. Use them as extra context."
-          local query_result = vc_cache.make_prompt_component(bufnr, component_cb)
-          local id = tostring(query_result.count) .. " file(s) from codebase"
-          codebase_prompt = codebase_prompt .. query_result.content
-          chat:add_message(
-            { content = codebase_prompt, role = "user" },
-            { visible = false, id = id }
-          )
-          chat.references:add({
-            source = "VectorCode",
-            name = "VectorCode",
-            id = id,
-          })
-        end,
-      }
-    end),
-
     ---@param subcommand sub_cmd
     ---@param opts VectorCode.CodeCompanion.ToolOpts
-    ---@return CodeCompanion.Agent.Tool
+    ---@return CodeCompanion.Tools.Tool
     make_tool = function(subcommand, opts)
       local has = require("codecompanion").has
       if has ~= nil and has("function-calling") then
diff --git a/lua/vectorcode/integrations/codecompanion/ls_tool.lua b/lua/vectorcode/integrations/codecompanion/ls_tool.lua
index 092aea50..32d77367 100644
--- a/lua/vectorcode/integrations/codecompanion/ls_tool.lua
+++ b/lua/vectorcode/integrations/codecompanion/ls_tool.lua
@@ -25,7 +25,7 @@ local get_ls_tool_opts = function(opts)
 end
 
 ---@param opts VectorCode.CodeCompanion.LsToolOpts
----@return CodeCompanion.Agent.Tool
+---@return CodeCompanion.Tools.Tool
 return function(opts)
   opts = get_ls_tool_opts(opts)
   local job_runner =
@@ -33,13 +33,13 @@ return function(opts)
       opts.use_lsp
     )
   local tool_name = "vectorcode_ls"
-  ---@type CodeCompanion.Agent.Tool|{}
+  ---@type CodeCompanion.Tools.Tool|{}
   return {
     name = tool_name,
     cmds = {
-      ---@param agent CodeCompanion.Agent
+      ---@param tools CodeCompanion.Tools
       ---@return nil|{ status: string, data: string }
-      function(agent, _, _, cb)
+      function(tools, _, _, cb)
         job_runner.run_async({ "ls", "--pipe" }, function(result, error)
           if vim.islist(result) and #result > 0 then
             cb({ status = "success", data = result })
@@ -52,7 +52,7 @@ return function(opts)
               data = error,
             })
           end
-        end, agent.chat.bufnr)
+        end, tools.chat.bufnr)
       end,
     },
     schema = {
@@ -73,9 +73,9 @@ Where relevant, use paths from this tool as the `project_root` parameter in othe
       },
     },
     output = {
-      ---@param agent CodeCompanion.Agent
+      ---@param tools CodeCompanion.Tools
       ---@param stdout VectorCode.LsResult[][]
-      success = function(_, agent, _, stdout)
+      success = function(_, tools, _, stdout)
         stdout = stdout[1]
         local user_message
         for i, col in ipairs(stdout) do
@@ -85,8 +85,8 @@ Where relevant, use paths from this tool as the `project_root` parameter in othe
           else
             user_message = ""
           end
-          agent.chat:add_tool_output(
-            agent.tool,
+          tools.chat:add_tool_output(
+            tools.tool,
             string.format("<collection>%s</collection>", col["project-root"]),
             user_message
           )
diff --git a/lua/vectorcode/integrations/codecompanion/query_tool.lua b/lua/vectorcode/integrations/codecompanion/query_tool.lua
index 906353dc..296c32ec 100644
--- a/lua/vectorcode/integrations/codecompanion/query_tool.lua
+++ b/lua/vectorcode/integrations/codecompanion/query_tool.lua
@@ -164,7 +164,7 @@ local result_tracker = {}
 ---@param chat CodeCompanion.Chat
 ---@return VectorCode.QueryResult[]
 local filter_results = function(results, chat)
-  local existing_refs = chat.context_items or chat.refs or {}
+  local existing_refs = chat.context_items or {}
 
   existing_refs = vim
     .iter(existing_refs)
@@ -316,7 +316,7 @@ When summarising the code, pay extra attention on information related to the que
 end
 
 ---@param opts VectorCode.CodeCompanion.QueryToolOpts?
----@return CodeCompanion.Agent.Tool
+---@return CodeCompanion.Tools.Tool
 return check_cli_wrap(function(opts)
   opts = get_query_tool_opts(opts)
   assert(
@@ -337,10 +337,10 @@ return check_cli_wrap(function(opts)
   return {
     name = tool_name,
     cmds = {
-      ---@param agent CodeCompanion.Agent
+      ---@param tools CodeCompanion.Tools
       ---@param action QueryToolArgs
       ---@return nil|{ status: string, data: string }
-      function(agent, action, _, cb)
+      function(tools, action, _, cb)
         logger.info(
           "CodeCompanion query tool called with the following arguments:\n",
           action
@@ -387,12 +387,14 @@ return check_cli_wrap(function(opts)
           end
         end
 
-        -- TODO: remove the `chat.refs` compatibility code when the upstream PR is released.
-        local context_items = agent.chat.context_items or agent.chat.refs
-        if opts.no_duplicate and context_items ~= nil and action.deduplicate then
+        if
+          opts.no_duplicate
+          and tools.chat.context_items ~= nil
+          and action.deduplicate
+        then
           -- exclude files that has been added to the context
           local existing_files = { "--exclude" }
-          for _, ref in pairs(context_items) do
+          for _, ref in pairs(tools.chat.context_items) do
             if ref.source == cc_common.tool_result_source then
               table.insert(existing_files, ref.id)
             elseif type(ref.path) == "string" then
@@ -421,7 +423,7 @@ return check_cli_wrap(function(opts)
           if vim.islist(result) and #result > 0 and result[1].path ~= nil then ---@cast result VectorCode.QueryResult[]
             local summary_opts = vim.deepcopy(opts.summarise) or {}
             if type(summary_opts.enabled) == "function" then
-              summary_opts.enabled = summary_opts.enabled(agent.chat, result) --[[@as  boolean]]
+              summary_opts.enabled = summary_opts.enabled(tools.chat, result) --[[@as  boolean]]
             end
 
             if
@@ -431,7 +433,7 @@ return check_cli_wrap(function(opts)
             then
               -- NOTE: deduplication in summary mode prevents the model from requesting
               -- the same content without summarysation.
-              result = filter_results(result, agent.chat)
+              result = filter_results(result, tools.chat)
             end
 
             local max_result = #result
@@ -457,7 +459,7 @@ return check_cli_wrap(function(opts)
               data = error,
             })
           end
-        end, agent.chat.bufnr)
+        end, tools.chat.bufnr)
       end,
     },
     schema = {
@@ -530,10 +532,10 @@ DO NOT MODIFY UNLESS INSTRUCTED BY THE USER, OR A PREVIOUS QUERY RETURNED NO RES
       },
     },
     output = {
-      ---@param agent CodeCompanion.Agent
+      ---@param tools CodeCompanion.Tools
       ---@param cmd QueryToolArgs
       ---@param stderr table|string
-      error = function(self, agent, cmd, stderr)
+      error = function(self, tools, cmd, stderr)
         logger.error(
           ("CodeCompanion tool with command %s thrown with the following error: %s"):format(
             vim.inspect(cmd),
@@ -543,7 +545,7 @@ DO NOT MODIFY UNLESS INSTRUCTED BY THE USER, OR A PREVIOUS QUERY RETURNED NO RES
         stderr = cc_common.flatten_table_to_string(stderr)
         if string.find(stderr, "InvalidCollectionException") then
           if cmd.project_root then
-            agent.chat:add_tool_output(
+            tools.chat:add_tool_output(
               self,
               string.format(
                 "`%s` hasn't been vectorised. Please use the `vectorcode_vectorise` tool or vectorise it from the CLI.",
@@ -551,13 +553,13 @@ DO NOT MODIFY UNLESS INSTRUCTED BY THE USER, OR A PREVIOUS QUERY RETURNED NO RES
               )
             )
           else
-            agent.chat:add_tool_output(
+            tools.chat:add_tool_output(
               self,
               "Failed to query from the requested project. Please verify the available projects via the `vectorcode_ls` tool or run it from the CLI."
             )
           end
         else
-          agent.chat:add_tool_output(
+          tools.chat:add_tool_output(
             self,
             string.format(
               "**VectorCode `query` Tool**: Failed with error:\n```\n%s\n```",
@@ -566,17 +568,17 @@ DO NOT MODIFY UNLESS INSTRUCTED BY THE USER, OR A PREVIOUS QUERY RETURNED NO RES
           )
         end
       end,
-      ---@param agent CodeCompanion.Agent
+      ---@param tools CodeCompanion.Tools
       ---@param cmd QueryToolArgs
       ---@param stdout VectorCode.CodeCompanion.QueryToolResult[]
-      success = function(self, agent, cmd, stdout)
+      success = function(self, tools, cmd, stdout)
         stdout = stdout[1]
         logger.info(
           ("CodeCompanion tool with command %s finished."):format(vim.inspect(cmd))
         )
         if vim.tbl_isempty(stdout.raw_results) then
           logger.info("CodeCompanion query tool recieved empty result.")
-          return agent.chat:add_tool_output(
+          return tools.chat:add_tool_output(
             self,
             string.format(
               "`%s` tool returned empty result. Please retry without deduplication.",
@@ -585,7 +587,7 @@ DO NOT MODIFY UNLESS INSTRUCTED BY THE USER, OR A PREVIOUS QUERY RETURNED NO RES
             "**VectorCode `query` Tool**: Retrieved 0 result. Retrying..."
           )
         end
-        agent.chat:add_tool_output(
+        tools.chat:add_tool_output(
           self,
           stdout.summary
             or table.concat(vim
@@ -597,10 +599,9 @@ DO NOT MODIFY UNLESS INSTRUCTED BY THE USER, OR A PREVIOUS QUERY RETURNED NO RES
           string.format("**VectorCode Tool**: Retrieved %d %s(s)", stdout.count, mode)
         )
         if not opts.chunk_mode then
-          local context = agent.chat.context or agent.chat.references
           for _, result in pairs(stdout.raw_results) do
             -- skip referencing because there will be multiple chunks with the same path (id).
-            context:add({
+            tools.chat.context:add({
               source = cc_common.tool_result_source,
               id = result.path,
               path = result.path,
diff --git a/lua/vectorcode/integrations/codecompanion/vectorise_tool.lua b/lua/vectorcode/integrations/codecompanion/vectorise_tool.lua
index 5291b8b7..0846738f 100644
--- a/lua/vectorcode/integrations/codecompanion/vectorise_tool.lua
+++ b/lua/vectorcode/integrations/codecompanion/vectorise_tool.lua
@@ -29,13 +29,13 @@ local get_vectorise_tool_opts = function(opts)
 end
 
 ---@param opts VectorCode.CodeCompanion.VectoriseToolOpts|{}|nil
----@return CodeCompanion.Agent.Tool
+---@return CodeCompanion.Tools
 return function(opts)
   opts = get_vectorise_tool_opts(opts)
   local tool_name = "vectorcode_vectorise"
   local job_runner = cc_common.initialise_runner(opts.use_lsp)
 
-  ---@type CodeCompanion.Agent.Tool|{}
+  ---@type CodeCompanion.Tools|{}
   return {
     name = tool_name,
     schema = {
@@ -66,10 +66,10 @@ The paths should be accurate (DO NOT ASSUME A PATH EXIST) and case case-sensitiv
       },
     },
     cmds = {
-      ---@param agent CodeCompanion.Agent
+      ---@param tools CodeCompanion.Tools
       ---@param action VectoriseToolArgs
       ---@return nil|{ status: string, data: string }
-      function(agent, action, _, cb)
+      function(tools, action, _, cb)
         local args = { "vectorise", "--pipe" }
         local project_root = vim.fs.abspath(vim.fs.normalize(action.project_root or ""))
         if project_root ~= "" then
@@ -118,22 +118,22 @@ The paths should be accurate (DO NOT ASSUME A PATH EXIST) and case case-sensitiv
               cb({ status = "error", data = { error = error, code = code } })
             end
           end,
-          agent.chat.bufnr
+          tools.chat.bufnr
         )
       end,
     },
     output = {
-      ---@param self CodeCompanion.Agent.Tool
+      ---@param self CodeCompanion.Tools.Tool
       prompt = function(self, _)
         return string.format("Vectorise %d files with VectorCode?", #self.args.paths)
       end,
-      ---@param self CodeCompanion.Agent.Tool
-      ---@param agent CodeCompanion.Agent
+      ---@param self CodeCompanion.Tools
+      ---@param tools CodeCompanion.Tools
       ---@param cmd VectoriseToolArgs
       ---@param stdout VectorCode.VectoriseResult[]
-      success = function(self, agent, cmd, stdout)
+      success = function(self, tools, cmd, stdout)
         stdout = stdout[1]
-        agent.chat:add_tool_output(
+        tools.chat:add_tool_output(
           self,
           string.format(
             [[**VectorCode Vectorise Tool**:
@@ -151,7 +151,7 @@ The paths should be accurate (DO NOT ASSUME A PATH EXIST) and case case-sensitiv
           )
         )
         if cmd.project_root and cmd.project_root then
-          agent.chat:add_tool_output(
+          tools.chat:add_tool_output(
             self,
             string.format("\nThe files were added to `%s`", cmd.project_root),
             ""