Ignore files when force:source:convert

Create a directory structure like donotconvert/main/default/permissionsets/ and move your debug apex permset under there. Add the donotconvert directory to the list of packageDirectories in sfdx-project.json. Now when you run force:source:convert specify the directory structure to convert using the -r parameter.

My read of the documentation is that the .forceignore file mentioned by others is only when you're pushing and pulling to the scratch org or converting from mdapi TO DX, not the other way around.

For our team where we just ran into this, I'm writing a bash script (but it could be written in anything) that will copy the DX force-app code tree to something like mdapimidway, prune out the files we don't want to convert and deploy and then call the convert command with the midway tree as the source to convert

sfdx force:source:convert -r mdapimidway/ -d mdapioutput/

The real power of DX isn't that it has functional parity with other tools, it's that you can throw it into the middle of your own scripts to take care of all the things they didn't think of.

Use .forceignore. As stated in the documentation:

When syncing metadata between your local file system and a scratch org, you often have source files you want to exclude. Similarly, you often want to exclude certain files when converting source to Salesforce DX project format. In both cases, you can exclude individual files or all files in a specific directory with a .forceignore file. (Emphasis added.)

Just had the same sort of problem and didn't find a mechanism in SFDX for this sort of filtering.

We are using Ant as well as SFDX and that has good filtering mechanisms (and we also have files split into separate trees so need to merge those trees) so we are first copying to a new tree of files where the files we don't want are excluded and then running the convert:

<target name="clean">
    <delete dir="./mdapi-source/staged"/>
    <delete dir="./mdapi-source/cvux"/>
</target>

<target name="convert" depends="clean">
    <copy todir="./mdapi-source/staged">
        <fileset dir="./sfdx-source/int/test"/>
        <fileset dir="./sfdx-source/int/main"/>
        <fileset dir="./sfdx-source/wiz/test">
           <exclude name="**/aura/**"/>
           <exclude name="**/staticresources/**"/>
        </fileset>
        <fileset dir="./sfdx-source/wiz/main"/>
    </copy>
    <exec dir="." executable="sfdx" osfamily="unix" failonerror="true">
        <arg value="force:source:convert"/>
        <arg value="--rootdir" />
        <arg value="./mdapi-source/staged" />
        <arg value="--outputdir" />
        <arg value="./mdapi-source/cvux" />
    </exec>
</target>

There might be something that helps in the sfdx-isv/sfdx-falcon-template project that:

This template can be used as a starting point for any Salesforce DX project, but has been specialized for building managed packages. Each directory in this repository contains a README file describing its purpose, what type of files it should contain, and additional setup/configuration details (if needed).