A simple solution (I should do this...)

1) Organize fastq files by project

group all your FASTQ into a UNSORTED bam : https://blastedbio.blogspot.fr/2011/10/fastq-must-die-long-live-sambam.html

the BAM will contain the sample name.

3) Annotate projects so you know what is what?

put some metadata into your BAM header: (like a code for your project)

2) Allow you to search for files

find the bam files extract the header and grep for the project. Something like:

find . -name "*.bam" | while read B ; do samtools view -H ${B} | grep PROJECT_NAME && echo ${B} ; done