Dear developer, I am sorry if the question is somewhat unclear. I am trying hard to find the best practice for the following: ##Keep my folder contents properly updated considering if I modify the folder heavily including adding a couple of files, moving around the files and folders, and deleting files. ###There are couples of upload and down options that make me sort-of confusing when to use them - Options for upload/download - `SyncFromSynapse`; `Synapse get -r synID (project/folder)` - `SyncToSynapse`; `Synapse-uploader -r remote\_folder\_name synID (parent) local/path/to/folder` - The`SyncToSynapse`/`SynFromSynapse` options seem a better way to go forward probably after the first Synapse-uploader. - However, I felt heavy to frequently update my file structures in the manifest every time I modify. Do it mean I need to frequently create and update the manifest probably by os.walk and format the tables. - Is there a better practice for that? ###And the problems are still lingering as the deleted files (in my local folder) will remain there in the synapse folder. - Do I need to manually remove them or is there a better practice? ### Could you kindly inform me how Synapse recognizes the same file and control the version? - Right now, I assumed that the Synapse recognizes the same file by file name and check the md5 to see if it is the same version? - With the `ForceVersion`, one may control the version to change regardless of the md5 status? - Is the mechanism the same when doing `SyncToSynapse`/`Synapse-uploader` ? I only test Synapse-uploader and it looks like it follows the first situation? ###Finally, if you can point me to useful resources, it will be great!!! - I have checked the following but not quite got the best way to work with complex folder structures. - **[Integrating Synapse in your RNA-Seq workflow](https://docs.synapse.org/articles/integrating_synapse_in_rna-seq_workflow.html)**: Using Synapse in an RNA-Seq workflow to manage files and track processing steps. - **[Download Data Programmatically from Portals](https://docs.synapse.org/articles/tutorial-download-data-portal.html)**: Use R, Python or the command line to download data. I am sorry to bombard the questions here. But I really need some input from your expertise to pull me out of the dilemma. Thanks ahead! Best, Minghao Gong