fix #9000 and #9006

Root Cause

It directly copies node_modules into the app directory and removes devDependencies from package.json. This way, npm list can retrieve all dependencies. However, during the lookup process, if there are duplicate dependency packages, some dependencies in npm may be empty. A previous fix（#8864 ） introduced the concept of implicit dependencies to address this issue, but it only handled the first level of implicit dependencies. If implicit dependencies themselves contain further implicit dependencies, the problem described in #9000 will occur.

How to fix

The current approach directly searches the parsedTree and updates the global this.productionGraph. If there are cases where dependencies are empty, it retrieves the same dependency from allDependencies and performs a lookup for sub-dependencies. If the dependency already exists in this.productionGraph, no further lookup is performed. Additionally, to prevent infinite loops, an empty array is set before searching for sub-dependencies.

Now that one tree lookup has been eliminated, there will be a certain improvement in performance.